[ay2b]

In your interrupt handler, are you clearing the interrupt flag? Are you clearing it in all cases (i.e. for every interrupt type)? Resetting seems a little odd to me, but I've seen cases where forgetting to clear the interrupt flag will cause it to run for a few seconds, and then freeze/crash/red-light-of-death. You said this correlates to changing a PWM value; you also said you have a gear-tooth sensor installed. If the motor is not running, you would be getting no interrupts. As soon as you change the PWM value, the motor starts running. This causes the gear-tooth sensor to start triggering interrupts. If you don't clear the interrupt flag in your interrupt handler, this will basically cause the system to overload, trying to repeatedly process the interrupt. In my experience, this resulted in a crash; in your case, maybe it's resulting in a reset.

Or maybe you have some other problem.