I understand this is an old topic, but I found a solution to this, so maybe somebody else googles this page and can use it:
1. Delete the "Output" Folder within the X-Plane folder in the steam folder
2. Start X-Plane
3. Go to the VR Settings in X-Plane and FIRST add "vr mouse" and only after that activate VR
4. With the mouse, go the the joystick tab, select your controller on the left and then press "set back to default values" or something like that. Then repeat step 4 with the other controller.
5. Then go back to the vr settings and deactivate the "vr mouse"
Worked for me in X-Plane 11 (11.20 I believe was the version).
Cheers
Tobias