[Noah Kleinberg]

Sounds like it could be a problem with your code? It would help if you could post the code in case that's the problem. You should try (if you haven't yet) loading the default code and seeing if the same problem happens, and also if this is happening on all of the PWMs or just the ones hooked up to your motors (or however you noticed this problem). You should also try another controller with the same code if you have an extra one somewhere, and then you'll know if it's a hardware problem or a software problem.