What do you think this noise coming from a Lionel Legacy S3 6-84065 is?

Does it do it on rollers?  I have an engine that makes  a similar noise on atlas track and the wheel flanges were hitting the nubs on the track ties. 

Have you greased the gearbox?

I've had a wiring harness rubbing the encoder wheel  on the fywheel making a buzzing sound as well.

For gearbox. Yes greased

Running on Atlas so perhaps but clicking is faster then speed of engine 

Just ran again but ran Hudson after it To compare

Thank you for the replies I have tried a few different things to try to eliminate it as per suggestions.  I have a buddy who has the ability to do it on rollers so may try that next and see what happens.   Engine works great other than this issue.  More annoying when this is the only one that does it.  

Both very smooth runners, I'm jealous!  In this case I don't personally think it's the driving wheel flanges on the ties, I feel like the frequency of the clicking is too high for that.  @MartyE what loco did you observe with this problem?

Two theories: (1) The plastic comb wheel that serves as the tach surface for speed control is rubbing on the sensor or something inside the boiler shell.  (2) What you're hearing is "slop" in the dog-bone shaft that connects the motor flywheel to the worm gear.  The dogbone could be toggling fore-and-aft in the cups of the U-joints.

To troubleshoot further you could run it with the shell off and observe.  That's the first thing I would do.  To quiet the dogbone, you could pack a little Vaseline or some viscous moly grease in those cups to stop the ball ends from slapping around.  But to totally rule out the dogbone you would have to remove it altogether.  Apply power to hear the motor and flywheel by themselves.

Honestly both locos seem to run great.  It's just a noise and I wouldn't be that concerned.  I don't know your level of mechanical skill.  But I would open it up for observation long before I would take the risk of sending it back to Lionel.  And yes, there are risks...!!

Thanks. Mechanical skills for what you describe maybe pushing it for me at least with newer engines. Spot on with frequency.  As a couple guys could not hear it or hear it well but both admitted they don’t hear higher frequencies well. 
Engine runs great just more my personal annoyance 

I’d still run it on another track type, tubular would be best.  You’d be surprised how long it took to figure it out. 

What I observed was the exact same noise. It's an easy check without removing the shell.  If nothing else it may save you some time.  

I had a similar issue on a slightly older Legacy steamer. Judging by the frequency/rapid pace of the sound, it's definitely coming from the area of the flywheel and could easily be a stray wire touching it as it rotates. In my case the flywheel was actually touching the chassis of the engine, which I figure came about as the result of shipping damage. It took some effort to create enough separation between the two parts to stop it happening.

In My opinion , it's either the worm gear not sitting correctly in the gearbox, or the flywheel encoder ring hitting the guard or the tach reader. The noise is going the same speed as the revolutions of the motor. 

Alex

@MartyE please- which Legacy loco(s) have the issue with flanges that are too large for Atlas track?

I believe it was my Santa Fe ATSF Northern.  After reading this thread though I may go back and check to see if I'm remembering my solution correctly.  I thought for sure it was the nubs on the track but maybe I did end up opening it and finding something.  Old age will do that.  LOL!  I'm pretty sure though I narrowed it down to the nubs but again I'll have to double check.

Hancock52 posted:

I had a similar issue on a slightly older Legacy steamer. Judging by the frequency/rapid pace of the sound, it's definitely coming from the area of the flywheel and could easily be a stray wire touching it as it rotates. In my case the flywheel was actually touching the chassis of the engine, which I figure came about as the result of shipping damage. It took some effort to create enough separation between the two parts to stop it happening.

Thanks.   I have not taken it apart so shall see.   

MartyE posted:

I’d still run it on another track type, tubular would be best.  You’d be surprised how long it took to figure it out. 

What I observed was the exact same noise. It's an easy check without removing the shell.  If nothing else it may save you some time.  

Will be running it this weekend on other types of track 

Thanks to all for your input.   Will run it this weekend with a few other operators to see what they think in person and go from there.   I ran it once more trying to determine location and still seems to be somewhere directly in front of the cab.   Will post back onto this thread future results or root cause hopefully when found.

Take the boiler off and I bet you'll see if anything is getting hit by the motor in short order 😉.

Did you find anything out about the noise?  Purchased a brand new engine and getting the same thing: https://youtu.be/d5jxhSkCia4

Took the shell off of my Southern 2-10-4.  The sound is still occurring- no wires touching anything. The sound is coming from the motor assembly. 

@WyattK posted:

Took the shell off of my Southern 2-10-4.  The sound is still occurring- no wires touching anything. The sound is coming from the motor assembly. 

Any chance you can post a video?....maybe we all can help you diag it...I had a noise coming from a Legacy Hudson, it was the crappy Cannon motor...it went bye-byes in favor of a Pittman....😁

Pat

@Ted S posted:

Both very smooth runners, I'm jealous!  In this case I don't personally think it's the driving wheel flanges on the ties, I feel like the frequency of the clicking is too high for that.  @MartyE what loco did you observe with this problem?

Two theories: (1) The plastic comb wheel that serves as the tach surface for speed control is rubbing on the sensor or something inside the boiler shell.  (2) What you're hearing is "slop" in the dog-bone shaft that connects the motor flywheel to the worm gear.  The dogbone could be toggling fore-and-aft in the cups of the U-joints.

To troubleshoot further you could run it with the shell off and observe.  That's the first thing I would do.  To quiet the dogbone, you could pack a little Vaseline or some viscous moly grease in those cups to stop the ball ends from slapping around.  But to totally rule out the dogbone you would have to remove it altogether.  Apply power to hear the motor and flywheel by themselves.

Honestly both locos seem to run great.  It's just a noise and I wouldn't be that concerned.  I don't know your level of mechanical skill.  But I would open it up for observation long before I would take the risk of sending it back to Lionel.  And yes, there are risks...!!

#2 is absolutely correct... I can confirm the issue is noise from the dog bone shaft. Greased it with Vaseline and sound is gone.  Thanks!

@harmonyards posted:

Any chance you can post a video?....maybe we all can help you diag it...I had a noise coming from a Legacy Hudson, it was the crappy Cannon motor...it went bye-byes in favor of a Pittman....😁

Pat

 Solved! Finally See above post.

Wow that's a lot of Vaseline!  if you haven't buttoned her up yet, you might want to wipe off some of the excess, otherwise the rotating shaft will sling it all over the inside of the shell.  Glad you found the source of the noise.

In looking at your photo, in your specific case the root cause is actually a mis-alignment between the motor, and the shaft coming out of the gearbox.  It's not extreme and the U-joints can compensate.  However- if it's possible to adjust the angle of the motor and there's room to do so, you could align them and make the problem go away altogether.

Haha, yeah I wiped some off. Just wanted to be sure at first that it dampened the noise. Yeah, it does look misaligned.  I'll see if I can get it straightened out like you mentioned. Thanks!

Forgot about this post.  Will try this solution.  Sent mine to local hobby shop and they couldn’t figure it out.  Just got it back from Lionel.  No repair needed sound normal. So will try your solution as noise still there

Thank you

@WyattK now that I can see this in full size, i also noticed that there's a screw missing from the rear of your gearbox cover.  And those wires look mighty close to rubbing on that flywheel.  That could cause noise too, and eventually rub through the insulation causing a short circuit.

For a while Lionel had gotten better about addressing these sorts of issues, but if you didn't address these issues before reassembling the loco, I would go back in and double-check.

@Ted S posted:

@WyattK now that I can see this in full size, i also noticed that there's a screw missing from the rear of your gearbox cover.  

Oh no, I took the cover off of the gearbox to remove the worm gear while fiddling around.  I only put the one screw in to hold the cover in place to make sure everything was working when I put everything back together (just so I didn't have to go back and unscrew all 4 again if it wasn't working correctly).  

As far as the wires go, I watched the flywheel spin freely without being attached to the worm and it wasn't coming close to hitting anything, but yeah anything can shift in placement after a while.  I'll keep an eye on it.

I've noticed that sound coming from my Milw. Road S-3. If I don't grease that u-joint will it damage or prematurely wear out?

@Paul Kallus posted:

I've noticed that sound coming from my Milw. Road S-3. If I don't grease that u-joint will it damage or prematurely wear out?

Good question!!  I have the Milwaukee S3 and would be interested if I should take action; didn't notice the sound on mine though.

@Paul Kallus posted:

I've noticed that sound coming from my Milw. Road S-3. If I don't grease that u-joint will it damage or prematurely wear out?

I don't think it would wear out.  The "cups" should be metal.  I'm guessing that the dogbone shaft is plastic.  If anything is going to fail, I think it would be the pins on the dogbone shaft.  That shaft is an inexpensive part used on several different models.  Even if it ceases to be available, specialty companies like Northwest Short Line, Stock Drive Products, etc., offer kits to make your own universal shaft in any desired length.

That being said... depending on your comfort level with taking things apart, warranty issues, etc., I would do the grease job just to be sure it's NOT a broken encoder ring, or wires rubbing on the flywheel.  My $.02.

@Ted S, ....I’m not 100% sold that greasing these cups is the “cure” for this condition....you hit the nail on the head with Wyatt’s loco as to where the noise was coming from, but I was more interested in the comment you made about the shaft alignment issue you noted, but y’all never did conclude if that was remedied ....free flying slinging grease, vasoline or whatever, seems like a band aid repair ....I’d like to see if someone can verify if there’s a bunch of slop between the dog bone and the slots, or if it’s a misalignment issue or what....I’ve put these dog bones in some builds almost to the max allowable defection with no grease, and to this day have no noise like that....and some of those builds have hundreds if not thousands of hours.....if the grease is the cure, fine, but I’m interested in knowing the offense that leads to that....

Pat

Guys: a dumb question or maybe I am a dumb guy, but I can't get the shell off and I am afraid to pry apart after removing a bunch of phillip head screws! Is there a secret to this S-3 shell removal? It is a very well done model IMO - fully rounded underside boiler.

Thanks.

Pat you're the master at motor alignment, custom mounts, etc., I know you know your stuff!  I think whether or not you get noise is a function of several things:

-The degree of misalignment (greater misalignment will cause the shaft to toggle back-and-forth more)

-The length of the dogbone shaft relative to the gap (too short = greater chance of noise.)  I've read some accounts where the shaft was way too short and it fell out, causing the loco to be immobilized!

-The size of the pins, relative to the width of the slots (small pins will chatter more, and allow more movement)

Yes, the grease is a band-aid solution.  But most folks don't have the skills to realign the motor, if there's even room to do so.  Nor to make a new shaft that's a better fit.  Wyatt posted a test run on another thread; it's very smooth and quiet.  If it were my loco I think I could accept it the way it is.

@Ted S.....ahh, yes,...I do remember a couple of locomotives with some discerning shaft issues....good point...99% of the time I wind up having to make custom shafts from brass tubing for my builds....therefore, I can carefully get shaft end play and phase the joints how I want them ( 180 degrees apart ) be interesting to see what’s the issue with some of these....don’t think it’s a widespread issue as there’s only a handful of complaints....if it turns out to be too short of a shaft issue, the better remedy ( without a bumpy trip back to Lionel) would be a custom shaft like this:......

Pat

Haha now you started the next great debate  ... whether the pins should be in the same plane, or at right angles!  I was always taught that they should be in the same plane, but I can see that you're a right-angle guy.    Maybe that's why yours are quieter, but this IS a subject for another thread.  One question though- do you epoxy the nylon shaft into the brass tubing, or just jam it in there with a press fit?

I use 3M panel bonder,......it’s a lot of overkill, but I never have a failure....JB weld ( slow set ) would work fine, .....of course, the trick is scuff the ends of the shaft, and scuff the bore of the tubing.....and prep clean with alcohol......the tubing is K&S engineering 7/32” ID tubing ....with either Lionel’s or MTH’s driveshafts, this is a very snug snug fit, so it aligns itself straight.....many ways to skin a cat, one could drill the pieces and pin them, but I like the clean look, and once the panel bonder sets, you’ll rip the brass in two before the shaft spins in the tubing.....

As far as the phase, yes that’s a topic for another discussion....being a mechanical engineer, I follow the millwrights guide....😉..

Pat

I dabbled with trying to realign my motor on the 2-10-4, but looks like I may break something before finding any success with that. I noticed after a bunch of laps around the track, the ticking noise of the dogbone started slightly coming back.  Put Vaseline down into the actual sockets of the u joints instead slathering it on top of the whole assembly.  We'll see how long it stays quiet.  

I messaged the repair man that fixed the rods on this engine about this issue. He said that he believes this is a common problem because Lionel doesn't have adequate protection in their packaging when shipping and the motor gets knocked out alignment... don't know how much of that is just speculation or truth. My guess is that it is just a shoddy build and improper quality control when these things are first being put together.  Maybe one day I'll fix the alignment issue. 

@Paul Kallus posted:

Guys: a dumb question or maybe I am a dumb guy, but I can't get the shell off and I am afraid to pry apart after removing a bunch of phillip head screws! Is there a secret to this S-3 shell removal? It is a very well done model IMO - fully rounded underside boiler.

Thanks.

@Paul Kallus, I'm not sure about the S3, but my 2-10-4 is also a model with cylinder smoke like the S3.  There are 2 screws, one in the bottom of each cylinder that need to come out if you haven't removed them (they are down in deep holes on mine).  Took me a while to figure out those were the last 2 screws I needed to take out in order to remove the shell. 

On mine, there are also 4 screws under the cab that need to come out as well.. so a total of 6 screws.  Again, I'm not sure if the S3 has a similar setup.

This has to have something to do with the driveshaft angles. I've got 9 MTH Premier steam locomotives with this same style of driveshaft/cup arrangement and they are dead quiet. Could even be that the knobs that stick out of the dogbone are smaller than the notches in the cups they fit into, so they slap around.

Its great that you were able to chime in with a solution to this older post WyattK.

Some many times folks never post a solution to an issue once its solved. Not realizing, they can help countless other modellers, months, or even years, later when it pops up on a search.

@RickO I think it is my old tech support background that I can credit.  I was obsessed with making sure the issue was fixed and that everyone was happy, lol.

@WyattK , do you happen to have a pic of the driveline before it got gooped up with vasoline or whatever it is you used?.....I’d like to see if there’s a solution without pollution....🤣

Pat

Can anyone share how the shell is removed? How much force after removing screws is required? Any tricks?

@harmonyards posted:

@WyattK , do you happen to have a pic of the driveline before it got gooped up with vasoline or whatever it is you used?.....I’d like to see if there’s a solution without pollution....🤣

Pat

Unfortunately I don't, but if you can see from that picture I posted with the Vaseline on it - the u joint on the flywheel is tilted up a little higher than the worm gear u joint. I tried repositioning the worm gear, but really no way else to change it's positioning.

@Paul Kallus posted:

Can anyone share how the shell is removed? How much force after removing screws is required? Any tricks?

@Paul Kallus you shouldn't have to pry the shell off hard at all - it should come right off if you have all proper screws removed.  If you are pulling firm on it and it isn't budging, it is still probably fastened down somewhere, whether it be from a screw or something else. 

@WyattK posted:

Unfortunately I don't, but if you can see from that picture I posted with the Vaseline on it - the u joint on the flywheel is tilted up a little higher than the worm gear u joint. I tried repositioning the worm gear, but really no way else to change it's positioning.

Hard to tell from that pic, since it looks like it just got finished eating a Krispy Kreme doughnut......two things could be the source of the noise here, as Ted mentioned, and I am seeing now.....too short of a shaft, or a poor alignment.....more side ways would be the issue, not so much as up & down ( on vertical plane) as I’ve mentioned before, I’ve put these dog bones at their max deflection, with no issues,.....hopefully Paul can get his shell off ( I’m not advocating that if it’s under warranty) and he’ll take some good pics of his issue....if it’s the same issue, of course.....then we’ll see if we can come up with a better solution than something intended to cure diaper rash....especially since WyattK’s is starting to make some noise again....to me, that’s no bueno....

Pat 

@harmonyards I'd be interested to see if we can come up with a good, non-vaseline solution.  👍

We’ll need to see one that’s not all covered in ‘Cerme de la diaper.....like I mentioned, at this point, let’s see if Paul finds the magical combination that gets his separated.....

      this will tell the story, if the shaft walks in between the cups a great distance, ie; it slides front and back almost to the end of the slots, ....then no bueno, ....if the pins bounce around in the slots too much, no bueno,....if the shaft is oober short, and there’s too much deflection, no bueno.....so what I’d like to see is a video with somebody using a toothpick, and see if the dog bone kicks around in the cups too much, and then rotate the flywheel by hand, and see how much travel occurs before #1; it starts to move the dogbone on the motor side, then #2; how much rotation it takes to start turning the gear box side.....that’ll be a good indicator if these things are overloaded with too much slop.......get the drift?...

Pat

I use that same style drive from North West Shortline. Their instructions say to make the drive shaft tabs parallel and not at 90 degree. Also when I install the drive shaft I loosen the motor mount screws so that when testing for smoothness I can lift the rear of the motor up slightly while running until the smoothest spin is achieved. I then shim the motor up by the amount of lift. It’s worth a try. This is of course after you’ve tested the motor without the drive shaft to ensure it’s not the motor. 

Rod, I won’t dispute what NWSL says to do with their kits,.....there’s more than one way to skin a cat, and that’s another discussion.....many theories on phasing....I know what works for me, and longevity with hundreds if not thousands of hours says I’ll quarter them....I can get some pretty steep deflections, but my end play and cup slots are snug and precise....never a slightest hint of noise......even with what some would consider ugly deflections......Pat

Pat, I agree. I’ve never had perfect alignment with this style drive. 

Wow a lot of action on this thread today!  @WyattK I agree that Lionel's packaging does a lousy job of protecting their trains.  But unless the screws were super-loose (and you would have noticed), there's NO WAY the motor "got knocked out of alignment in shipping."  Lionel uses this same style of cast-in idler gearbox on several different locomotives.  The alignment was probably right for the first model with this setup.  But they declined to spec out a larger worm wheel or make other changes for the 2-10-4.  I'm guessing there's not enough room to tilt the motor to get perfect alignment.

And it's not only Lionel.  @Lou1985 I have a Premier 20-3130 (the first Reading T1.)  I'm not sure if MTH reused the chassis geometry from the N&W 'J' or what.  But the motor-gearbox alignment isn't even close, and they are both non-adjustable.   The dogbone shaft chattered like a telegraph key when the loco ran in reverse, I almost returned it!  I ended up creating a little extra clearance for the thrust bearing at the rear of the gearbox by removing part of the fiber gasket.  But the designers should be ashamed at the mechanical ugliness they created!  If it wasn't boxed up and buried in a closet I would post a pic.  I've never seen a newer T1 with its shell off, to see whether they improved the alignment in a later release.

Bottom line- the design is typical of die-cast, mass-produced toy trains which favors re-use of existing molds.  The way the chassis is designed, with a built-in gearbox and captive axles, is already inferior to the approach used for decades on scale models.  They can get away with it because the driving axles are unsprung, so there is no requirement for the geared axle to move independent of the others.  Unfortunately, this type of gearbox can't rotate to line up with the motor.  Thankfully, the dogbone shaft can handle some pretty extreme misalignment!  I'm thinking if you get a slightly longer shaft from Lionel, or make a custom one as illustrated in Pat's photos you'll silence the problem permanently. 

Note: Northwest Short Line (NWSL) sells several kits with the horned balls in different sizes.  A ball with larger pins may also be part of the solution.  Interesting discussion!

But the motor-gearbox alignment isn't even close, and they are both non-adjustable.   The dogbone shaft chattered like a telegraph key when the loco ran in reverse,     ( Ted’s quote ☺️) 

everything is adjustable Ted,.....that’s why on the seventh day, they made machines....😁😁😁

Pat

Well.. the noise has come back.  Guess the vaseline has thinned out enough to let the dogbone flap around noisily again.  I have greased it with vaseline twice now.  Any other ideas for a fix?  Would wrapping a thin layer of electrical tape around the pegs of the dogbone keep them from flapping so much? Might try that next.

Electrical tape would last about one lap around the layout!  If the noise bothers you that much, it might be time to invest in some better U-joints and a proper driveshaft.

Ugh. Yeah, I'm thinking I should've sent this engine back for good for a refund so I can get a new one without this problem.  I got a good deal on this one brand new though. Guess the huge discount is worth dealing with a little noise until I get it figured out. 

I’m still waiting to see some good pics of one with out all the good on it to propose a proper solution....

Pat

Wyatt if you exchange yours for the same model it might have the same problem.  It's a flaw inherent in the design, perhaps because Lionel re-used parts and dimensions from another loco. 

A new custom drive shaft that fits more snugly, larger pins set at right angles to each other, etc., would be a permanent solution.  Any skilled repair person can make one or you can even do it yourself.  See Pat's (harmonyards) pics on page 1 of this thread.  Sorry you're having frustration, hope you can get it worked out to your satisfaction!

@harmonyards, might take the shell off again tomorrow and see if I can figure something out.  I'll wipe all the Vaseline off and post a pic.  @Ted S, Hopefully I can get something worked out like that. Thanks.

@WyattK posted:

@harmonyards, might take the shell off again tomorrow and see if I can figure something out.  I'll wipe all the Vaseline off and post a pic.  @Ted S, Hopefully I can get something worked out like that. Thanks.

Just clean it all up, and put it back together stone stock like it was....noise and all,....I’d like to see some key points on the coupling set up and build it better than they did....clearly snotting it up with Vasoline at least identified the issue ( good find Ted) ....now we’ll come up with a permanent repair that can be repeated incase others have the same issue....I guess the other fella never could get his shell off??...I haven’t seen him reply back, unless I missed him...

Pat

WyattK, hang in there; have had harmonyards repair 2 old Lionel track cleaning cars for me - better than new; the fellas on this forum will help you fix anything.

I vaguely recall a thread where someone had a TMCC or legacy steamer that made a similiar buzzing sound when going down grade.

I believe Mike Reagan chimed in and suggested bending the motor mount slightly to make the driveline straighter and it fixed the issue. At the time he stated this was a somewhat common problem and that was the prescribed" fix".

I have no clue if this is possible on the S3.

@RickO Yeah, I was actually going to look into possibly unscrewing the motor mount and seeing if I could bend the tabs at the bottom, but this dogbone drive shaft chatter may possibly be because the dogbone pins are too small for the u joints like they were saying, so they just bounce and slap around while spinning.  Though I think Ted or someone pointed out my motor mount is definitely misaligned. 

Come to think of it.

There was also another loco released in the recent past where the dogbone was too short.

I can't find the thread. I believe one members crude fix was to stuff something into one end of the coupling to stop the rattling back and forth.

@RickO posted:

Come to think of it.

There was also another loco released in the recent past where the dogbone was too short.

I can't find the thread. I believe one members crude fix was to stuff something into one end of the coupling to stop the rattling back and forth.

You are correct Rick, ....it was John Rowlen that had one carrying on, and he found the dogbone was too short,....another boo-boo band aid fix,....but it did silence the locomotive enough to determine that was the cause....he stuffed paper behind the coupling....but I’ll be ****** if I can find the thread either....

Pat

I also had a problem with a dogbone being too short. It actually broke the pins off.  The motor mounts could not be changed due to clearance in the shell.  I ordered a new dogbone and same issue.  I also ordered the next size longer from Lionel and it was too long. I looked at moving the coupler joint on the motor shaft and on the gear box shaft closer, but these were also fixed in place and not easily moved.

So, I purchased small plastic pellets used for pellet gun and sanded them in half.  I bonded one in the motor coupling and a 2nd in the gear box coupling. This positioned the dogbone in the "middle" so to say. I wanted to use something that was rounded and would not bind. There remained a slight clearance for movement in the dogbone.

This did the job. And the engine ran well without any noise. 

If I was to redo this, I am not sure I would do it again or do what Pat suggested.   I do like what he has shown. But I also have a bunch of extra pellets... 😁

Thanks for the tips on getting the boiler off...have to confess this was a puzzler, but its always a case of jimmying here and there after removing screws. I didn't add any grease to mine, though, given what I've read here. I forwarded the link to this thread to Dave Olson at Lionel...hopefully he can respond at some point.

All,

It took me a while to find the photos of my repair.  I have attached in my earlier post.

Hope this helps.

Best, Dave

Lionel used to use metal driveshafts in their locos. At least up to the first generation of legacy stuff.

Given the torque on the shaft. It would seem there could be failure of the plastic pins at some point. Especially as the Loco ages.

That old tmcc Hudson I purchased (on another thread) sure has a nice quality drive line. 

Dave I'm glad your repair worked, but personally I wouldn't want glue anywhere near my motor or flywheel.  If the motor ever needs to be replaced (and sometimes they do), that could make it difficult to remove the flywheel and U-joint coupling.

The driveline in the S3 or Wyatt's Texas type on the other thread isn't lower quality than what Lionel was using in 2001.  In fact, many of the newer gearboxes are back-drivable (the wheels can turn the motor), which is a worthwhile improvement.  Problems like the tapping noise occur because Lionel re-uses standard parts like the dogbone shaft, and even the gearbox geometry; the gears themselves; the angle of the worm shaft, etc., that were originally designed for other locos.  Perhaps in its original application, the motor was further away or mounted at a different angle which matched that of the worm shaft. 

If we're correct about the cause of the problem, then it's absolutely not a big deal.  I'm convinced that if you, or a repair person make a new custom drive shaft of the correct length, with thicker pins set at right angles to each other, you'll never have this problem again!