To eliminate interference from the issue - remove the encoder from the motor shaft. The counts should not change regardless of what the motor is doing. I would expect the interference is not the problem and I would agree it is resonances and inertia causing the extra counts. To confirm this, you could mount a disk with a index mark on it and have a piece of wire or something similar to line up at a given position. If you step forward a number of steps, then step backwards a number of steps, repeat this a few times and see if the mark still lines up. Then modify your software to use the encoder counts rather than the motor steps and do the same operation. This will tell you if the encoder is lying to you. Obviously, the more fwd/rev cycles you do, the error will increase, so this should guide you as to the magnitude of the problem.



With steppers, I learnt some time ago that they are not quite the wonderful device you like to think they are. Resonances are one such problem.