A quick use of the search (with the error "waiting for cRIO to reboot" in the search box) reveals this thread from last year:
http://www.chiefdelphi.com/forums/showthread.php?t=100022&highlight=Waiting+for+cRIO +to+reboot
we had the same issue at some point, it really is annoying! But it forced us to use the output on the Driver Station, so now we use both. Every problem is an opportunity to learn a new skill
