We are running Windriver and expierienced the same problem. We had put the new image on and the cRio was recieving our code. When we booted the driver software we recieved a no code error. We fixed the problem by taking this link
http://first.wpi.edu/FRC/frccupdates.html and then running this update. "The mandatory LabVIEW update contains the new images and imaging tool to work with Java or C++." We reimaged the cRio once again and no longer had a problem.