Our team just recently encountered this same issue with our 4-slot cRIO. We found that a reliable way to fix it was to FTP into the cRIO (using just the IP, no password), going into "ni-rt", and deleting the "startup" directory. It fixes the problem every time, although the cRIO sometimes has to be rebooted first.
I'm not sure if that's what "Unset as startup" already does, but I know it works for us.
