We had a very similar issue before. If the cRio does not like the code, it will display the "No Code" message. Have you updated your WPILIB files yet? There is an update for WindRiver on the FIRST website that will upgrade your library files to the new revision. My understanding is that it might change some of the example projects. If the examples have the wrong code format, it might not be compatible with the cRio updates.
Go here:
http://first.wpi.edu/FRC/frcupdates.html and download the workbench updates.
I think that if you can download code your connection and transfer are solid. It just sounds like it's a code problem.