Enable NetConsole with the cRIO Imaging Tool, then tether up, run it and look at the output after a deploy + warm reboot versus a cold boot. Definitely want to be tethered, as the cRIO could boot faster than you'd get a wireless connection. If everything is as it should be, then the output on a warm-reboot vs a cold boot should be identical. If it's not, the we have information to work from.