It sounds like you're trying to run the code in debug mode rather than burn it to the cRio. If you run it through debug, then the code will be on the RAM but will not stay on once you turn off the cRio. Try running FIRST->Download when connected to the cRio in Windriver (although burning code through FIRST->Download hasn't been working for out team either... but that's another issue entirely)
Also, did you install the update for the driver station according to the following post:
http://www.chiefdelphi.com/forums/sh...9&postcount=44
Finally, how do you have your connections set up? Are you directly connected to the cRio by ethernet, through the gaming adapter, or through the wireless bridge?