In my experience this is normally caused by a situation where the UI thread on the RT (responsible for communicating back to your PC) is starved, resulting in communication failures. Starving could be the result of a number of things but typically it is caused by other code running at a higher priority (eg. Timed Loops, Time Critical priority VIs) and that code occupies the entire CPU - the UI thread isn't given any time. Take a look at this (http://www.ni.com/white-paper/14/en/) which gives some background info.
Simply put: When you deploy and run a VI on the RT it runs it temporarily (until you stop it) and it doesn't run on RT startup (you need to build a startup application to do that). When you run your VI temporarily the RT UI thread needs CPU time to communicate back to the Front Panel shown on your PC as well as communicate block diagram and probe data if you are debugging. Anything that prevents the UI thread from getting CPU time to do this will cause your PC to lose communications to the RT, most likely tight loop(s) that leaves little CPU time for anything else.
If you post your VI (or an example that you think causes the issue on occasion) then we might be able to provide better direction.
