We have experienced that before. Basically, the NXT was hung. In our case, it was because of a bug in RobotC. I reported the bug and they confirmed and fixed it. But they could not release the fix yet. So we rewrote the code to avoid the bug.
http://www.robotc.net/forums/viewtopic.php?f=52&t=2712
You may have an entirely different problem. But the point is software can hang the NXT brick.