I had some weird similar problems and the calib I did on X1 did not take. However I found these instructions on a post here that solved my issue. It has a step I had not used before, so give it a try. I saved instructions knowing I would need them again.
1. Ensure DJI RC System Assistant software is Installed
2. Start the DJI RC System Assistant software, plug the controller into USB port and power it on. Sometimes if the controller is plugged in before the software is started, it won't recognize it.
3. Click 'Calibration'
4. Click 'Next' after ensuring you are not touching any of the levers or sticks on controller
5. Move the left and right sticks in a circle a few times to reach their limits
6. Move the X1 lever on the back of the controller back and forth slowly a few times
7. Press 'Finish'
8. Close the DJI RC System Assistant software and disconnect the controller from USB port
9. Start the DJI Phantom 2 Assistant software
10. Plug the Phantom 2 into USB port and power it on
11. Click 'Basic' at the top and select 'RC' beneath it
12. On the right hand side, select 'Start' in the X1 Calibration section
13. Move the X1 lever on the back of the controller back and forth slowly a few times
14. Press 'Finish'
15. Select 'Start' in the Command Sticks Calibration section
16. Move the left and right sticks in a circle a few times to reach their limits
17. Press 'Finish'