I think we had "bad" breakers. I'm not sure what exactly that means but when we replaced all the 40a with new breakers the RoboRio started doing what it is supposed to do and turned the motors off. It is now keeping the rest of the systems running. I have no idea how changing the breakers could do that. Maybe something else got moved around while changing the breakers.
RufflesRidge: I believe we we're dropping near 5v at some points.
Joe: Chain may fix this for us. Thanks for the suggestion. Also...your cutting ABS sprockets for drive trains

As someone who loves laser cut ABS that never occurred to me. About 40% of our robot last year was ABS. Do they hold up as sprockets?