[Jared]

Reformat/reimage the roboRIO. I had a really, really weird intermittent CPU usage and CAN bug that went away immediately after I deployed code or restarted it, but came back if I power cycled the roboRIO. It's exactly like you're describing- the code doesn't work right if the robot starts from a cold boot, but it works if the code is started after the controller fully powers on. Something different with CAN happens when the code is started by the deploy sequence vs. a cold boot.