PWM is dead (Mega)

Well, this is my first time working with the Arduino platform. I took to it pretty well, and my team at school built a bot for a competition. Everything was working great all semester. 10 pm before the competition our PWM pretty much just quit. It would just give out junk. We unplugged every other system besides the motors and the motor shield, and it still didn't work. Then we took an Uno board we had, with the exact same code and the same motor shield, and it worked great. My only guess is that the PWM circuit on the Mega got fried. Before we trash the board, just want to know if anyone else has encountered this problem before and if you found a fix. We'd also like to wipe the board and start over or do a hard reset, but we don't know how. Any help or suggestions?

Are you able to upload Sketches to the dead board?

Yes, in fact we can still read sensor values from a serial print, and it's calling the correct functions to run the motors (we even set it to JUST go forward). And like I said, same code, same motors and motor shield, it works great with the Uno.

Correction, I said it was the same code, the pins were changed, i.e. they were plugged into the correct pwm pins on their respective boards.

If you can, try running something very simple like fade...

Does that work?

On the dead board, do the PWM pins work as normal digital pins? Are you able to turn an LED on / off using the PWM pins?