Check the CPU usage first so you know what's happening there.
I assume that after you reimaged the cRIO with the 2011 v25 that you didn't download any robot code?
So there shouldn't be anything running on the cRIO and the CPU usage should be close to the bottom.
Does the timeout message stay up for a long time? It's normal to see it occasionally and it'll usually go away within 20 seconds or so.
Here is something else to try after school for the timeout error you're seeing:
- Flip the NO-APP DIP switch on the cRIO and reboot it (reset button or cycle the power), then turn the NO-APP switch off again.
- Then try the Run button.