[Alan Anderson]

The repeated initialization message says that your program is causing the Robot Controller to reset repeatedly. squirrel probably has it pegged: the current draw from the motors drops the voltage to the point where the RC doesn't have enough to keep running.

But in case that's not the problem, which timer are you using? How long did you set it to run before causing an interrupt? Did you remember to reset the interrupt flag in the service routine?

One more thing: are you using PWMs 13-16? Using the standard IFI code, those four outputs don't play nice with interrupts.