After reimaging the CRIO, programs must be redeployed. So what you are seeing is expected behavior.
The best place to check for software updates is here:
http://www.usfirst.org/roboticsprogr....aspx?id=18758
At regionals, they are checking for latest CRIO image and latest Driver Station program. So save yourself some angst and try to have these updated before getting to the competition.