I don't know if this could apply to your case but that is the way I calibrate my radio in ubuntu:
- Install (if you haven't already) the jstest-gtk package
- Plug your radio in the PC and launch jstest-gtk program
- Center all sticks then do the calibration within the program
- Now, exit from jstest-gtk without moving the sticks and launch FPV Freerider
- Go to the controller calibration, keep the sticks centered until requested to move them
- Do the calibration stuff...
Now the radio should be correctly calibrated... try and let us know.