C++ Code is not detected by the robot

[peronis]

So this problem may sound a little strange, and I'm really not sure what the issue could be at this point, so I'll try to explain in the best way I can and hope that someone here can help us fix the problem. Simply put, when the code is deployed to the cRIO and then rebooted, the driver station fails to recognize any code on the robot. I know you're all going to say to try reverting back to an older version of the to ensure it's not a hardware issue, so let me put you at ease by saying I have already tried. Older versions of the code work. Specifically, the robot detects code on some older versions, but after someone people cleaned the wiring, none of the motors seem to work. I suspect this is unrelated, as we had the same issue before we cleaned the wiring when we tried implementing PID code. I created a new workspace and began implementing subsystems piece by piece until the issue appeared again. Our drive system works, our subsystem to get the ball works, but once the PID code is used, the problem reappears. However, if I work backwards from the completed code, and simply remove the PID subsystem, the issue remains. The driver station indicates no robot code, and it therefore cannot be used. I intend to post some of the code in question here soon. Particularly the PID code, which I have a poor understanding of to begin with.

Note that the code is command based, and the prime issue is almost certainly in the code itself.

Any help here would be greatly appreciated.
--Tim the Enchanter, 3950 (aka TK3950)