[Alan Anderson]

Without seeing the exact sequence of what's happening to you, I can't be sure, but I have a theory. If your program is keeping the cRIO extremely busy, it won't be able to respond quickly to the programming computer's attempts to communicate with it, and LabVIEW will complain about communication problems. It's easy to overwork the cRIO like that -- all you have to do is forget to put a little bit of delay in a neverending while block. Check your code for fast-running infinite loops and see if you can't slow them down a bit.