1. What is your Robot Signal Light doing when you boot normally?
2. Are you deploying code to the cRIO and not just running the code with Labview's run button?
3. Has a mischievous gremlin switched the No App DIP switch on your cRIO? (Sorry, don't recall how the correct position looks)
EDIT: See page 12+ of this document for DIP switch settings:
http://decibel.ni.com/content/docs/DOC-2632
Make sure Safe Mode, No App, IP Reset, and No FPGA are all OFF.