You might have better luck posting in the FTC specific forum.
http://www.chiefdelphi.com/forums/fo...play.php?f=146
Are you using labview or RobotC? If you're using labview, and I don't know for sure if this could be an issue, it's just a guess, I've heard of teams either maxing out, or coming close to maxing out, the NXT's memory. I wonder if you just have too many programs on the NXT.