Thanks for the answers!
I don't think it is the motors moving against each other, because they WILL spin, but they lose signal. Hard to explain but we definantly made sure they were not moving against each other.
The gearbox is fine because again, they do work, but it's only in one direction. I'm thinking it is an electrical issue.
As per reformatting the cRIO, we didn't really know what to do so that was one of our last options. And we've rewrote the code several times with and without the watchdog.
What exactly do you mean by supply power to the digital breakout? This sounds like it could be the problem. Is this a module on the cRIO or is it on the digital sidecar itself. Noob question, I know

. It's been a while.
Thanks for the answers though!