[RyanCahoon]

I would agree that what you are describing sounds like back-EMF is damaging the microcontroller. The inline resistors will help protect against this some, but it's still possible that enough current could pass back through them to damage the control logic (can't be exactly sure without knowing the value of the resistors and what their current rating is). What I've seen a lot of people do when constructing circuits like this is to use opto-isolators between the microcontroller and the motor drivers, which is a pretty standard way of eliminating back-EMF.

Like was mentioned, I would suspect that after the circuit stops working, that the program is actually still running but since the port circuitry is damaged you won't see any output. If you're certain that the code is not actually running, it's possible that instead of the microcontroller, some of the power/clock circuitry could have been damaged. Usually the PIC Programmers supply their own power and clock signals, so this would account for it working while programming, but not otherwise.

Good luck,
--Ryan