[TDohse]

That error shouldn't actually cause any problem for running a LabVIEW program. It means the cRIO is configured to expect to find a file (startuppatch.out) in flash, but the file was missing. It's not a critical file, you can program/compete without it.

However, it's still very strange that you're seeing this. Have you been removing files through FTP or manually editing the ni-rt.ini config file on your cRIO? Also, could you explain what steps you took when reimaging your cRIO? Have you gone back and forth between C++ and LV, or toggled between having the "Always run deployed code at startup" option on and off?

It would be very helpful if you could post your ni-rt.ini file to this forum (FTP to your cRIO, it is in the root directory).