[Alan Anderson]

If it is due to quick changes of direction, as you suspect, then the way to fix it is to use software to limit the rate of change of direction.

Here's one possibility: Whenever you're going forward, keep a "reverse limiting" value reset to zero. Whenever you're not going forward, let that limiting value decrease at a constant rate toward -1. If your current joystick value is less than the limiting value, send the limiting value to the motor instead. Do the same thing but upside down for "forward limiting".