Here's a highly relevant thread from last year:
http://www.chiefdelphi.com/forums/showthread.php?t=84725
I'd lean towards one of your motors having developed a short or a short to ground that's intermittently blowing the breaker to your cRIO, or possibly your digital sidecar. You're quite clearly not losing main power. If you'd lost all power, you'd be down for a good 45 seconds or more while you waited for the bridge to reboot and reconnect. I'd check resistance from all your motors to your robot frame and try giving your robot a 1 foot drop and see if you lose communications. If you do, start pulling breakers for motors till you find one that seems to fix things, and inspect all the wiring after that breaker.