[k4mc]

Perhaps you have a memory leak that is causing the processor on the cRIO to reset every 64 seconds? That would explain why you don't loose communication but everything else resets and could be likely given C++ doesn't have a garbage collector.

You could at least easily test if this is the issue by downloading sample code onto the bot and waiting 64 seconds.

Edit: I just noticed you said that sample code removes the problem, so I now highly suspect something in your code is periodically crashing. If its not a memory leak, you could try first uploading an empty file and slowly adding one class/file/functionality at a time to see which part is causing the crash.