Blinking Jag lights mean (among other causes):
- The code has not opened that particular PWM port (could be due to the module being in a different place than the code expects)
- Or the robot is Disabled (you did say it was user enabled, but if your Driver Station status is Watchdog or system Disabled for Safety vi timeout or some other reason)
- Or there is no power to the digital sidecar (check that all three battery lights are bright green)
- Or PWM cables are reversed or otherwise not fully connected
- Or the cRIO isn't running
If you get the Jag lights to go solid, then a continued lack of control could be something even simplier.
Your xbox controller may not have defaulted to the USB port you expected.
Look at the Driver Station Setup tab to see which USB (1-4) your Xbox controller ended up on. Pressing any button will make it turn blue on the Setup list.