I have a really odd issue with the 6-35482 R-30 Subway powered unit.
The symptom is jerky running, especially down grades. Upon inspection, I saw that the encoder wheel was actually rubbing on the bottom of the sensor slot. "Easy fix" I though, I just moved it up. That seemed to cure it.
I got it back, same problem. Sure enough, it still has the same issue, even though I ran briefly here looking good. OK, maybe the end play of the motor is too much, so I ordered a new motor.
New motor installed, SAME PROBLEM! OK, now there's no encoder rubbing, and as it turns out, the end play of the new motor is the same as the existing motors, both front and rear. It's also less than 1/16", so it's probably not end play.
OK, I skywired the motor and encoder to my RCMC test set and used a totally different motor driver to drive the motors. STILL THE SAME PROBLEM! Tested the old motor on the test set, and ... same behavior!
OK, now I've eliminated the motor/encoder and everything else! What do I do next? I have run out of suspects!
I do notice that the motors in this set exhibit excessive "cogging" when you turn the flywheels manually. Since a new motor and running with a whole new electronics package doesn't seem to fix it, the only thing I can come up with is the factory used a bad choice of motor.
Note that my testset uses the exact same encoder board on a different Mabuchi motor type, and it's butter smooth running there. Also, the motor on the testset exhibits minimal to no cogging when manually turning the flywheel.
The back story is this issue was there from the time the customer got the set new, that was obviously in around 2009.