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Are you using the FPGA? If so, did you recompile after making some minor changes? What changes did you make?
I get that fairly often on cRIO, too. The main cause is I forget to include a time delay in a loop somewhere. Sometimes, I just have too much processing to keep up.
The cRIO (and I'm certain the myRIO, too) has an operating system that tries to divy up time among several tasks. One of those tasks (and probably with the highest priority) is your application. Another task is keeping communication with LabView on your computer. If your application doesn't give up enough of the CPU, then the communication gets starved, and drops links.
You can probably check the web-page generated by your myRIO, to see what the CPU usage is.