I had a similar problem with my 8305 Milwaukee Road locomotive. It would sometimes not work in reverse, or would stutter in reverse. It turns out it was a bad/cold solder joint for one of the wires connected to the motor assembly.
It took me quite awhile to find the problem, as I was originally thinking it was a problem with the e-unit. I finally found the bad solder connection by doing a "tug test" and just tugging on the wires to the motor. One of the wires came loose after tugging on the wire. I re-soldered the wire to the connection point on the motor and have not had a problem since. Not sure how prevalent this problem was for these locomotives, but I'd check that out as the cause of the problem. Here is a diagram and area with the wires and solder connections to check:
I first observed this issue back in the early 80s, and remember being frustrated as a kid that my locomotive was having this problem. I finally figured out and fixed the problem 35+ years later. 
