[Warren Boudreau]

Sounds like there is an answer somewhere in here.

Our normal debugging goes like this:
1). Is it software? Always blame the software guys first....
2). Check that each motor is working by itself. (a wiring problem)
3). Make sure that the motor pairs are driving in the same direction. (a wiring polarity problem)
4). While propped up on a stand see if you can see if one side is running faster than the other. (a gearbox or drivetrain problem).

After that, you should have a good idea of where the problem lies.
We have been using the drill motors and CIMs combined for several years now and have not seen a problem like you describe.