This actually happened to us during the Michigan Competition. It reached the point where it was so bad, that our entire robot shut down for 3 hours.
Heres what you can do. First try reloading the code, including the VEX master 2007 code. If that doesn't work, unplug all of your pwm cables, and try one by one to see which ones are functional (drivetrain, then arm) and which ones are not. From that, you can at least determine the problem.
If you still have a problem, you can email me at
fredliu168@hotmail.com or PM me on CD. I'll try to help out as best as I can.