I was just about to post a BREAKTHROUGH thread about a magic trick I learned today because I was getting your exact same problem today at the Arizona Regionals.
... send $100 to my paypal account and I'll PM you ...
OK, here's the magic trick that NI's rep gave me today ... [I'll edit this post with with Kudos (and his correctly spelled name) after I see him tomorrow]
1) on the cRIO, set the
No App dipswitch to TRUE (this prevents user code from running when the cRIO boots, regardless of the SW settings)
2) reset the cRIO and feel free to deploy/run/build/set-as-startup, whatever ... As long as that dip-switch is set, it'll never run the startup apps when it boots, and the deployents (or just hitting RUN in the RobotMain.VI) works every time.
3) when you are done debugging and/or troubleshooting and want to try it out in a "realistic" fashion, do a final build and Set as Startup.
4) when the upload to the cRIO is complete, there's a window to close and then it asks you to reboot the cRIO. Before you click the Reboot button, UNSET that dip-switch
He said that they are looking into why this is occurring, but apparently they've got a pretty good workaround until we get a patch.
After I learned this trick, I never saw those errors again, and we were slinging code onto our 'bot all day today (Practice day at the AZ regionals)
Hope this helps.