Your description sounds like the NO APP switch isn't getting set properly.
To use the NO APP switch:
- flip it to ON
- reset the cRIO (3 equivalent ways)
- cRIO panel black reset button
- DS Diagnostics->Robot reboot...
- cycle power
- After the DS Comm light comes back on, then you can flip the NO APP switch back OFF. You don't have to though until you want the user code to startup automatically.
If you get the NO APP switch working, then you can move on to discovering why you have to use it in the first place.
Usually, it's only necessary if your code is running too fast and hard. There are ways to check on that.