DS doesn't recognize robot code in startup application

[kamocat]

I have a robot project that I've modified.
When I open up Robot Main and click the run arrow, it deploys, and the driver station recognizes the robot code. I can enable it. It works. (Well, autonomous seems to work better than teleop, but I think that's just issues with the throughput of the CAN bus.)
I build and deploy it as a startup application, and say "yes" to the cRIO reboot. The DS connects, but it won't recognize the robot code even after several minutes.

I make a new 2010 game competition project. The DS doesn't recognize the code in the "open and run" or the startup application.


I'm pretty sure I need to reinstall some things, but I'm not sure to what extent. Is it just the FRC libraries?
(I'm guessing it's not the DS, considering it hasn't had any changes since the last DS update, and it works identically to the one on my own computer. However, after an accident with Linux and my partition table, I've had to reinstall Windows and LabVIEW and all on my Macbook. No more triple-booting for a while.)