Many games can‘t handle simultaneous mouse/gamepad input. Sounds like such a case.
If you want mouse based head tracking in affected games and still play them with your gamepad, you can use vorpX‘s built in configurable gamepad to mouse/kb mapper.
The X-Box Gamepad Override option has to be set to On for that. If necessary you can then configure the mapping to your liking. In some lucky cases you might get away with a partial override of just the right stick and leave the rest of the gamepad native.
If you don‘t want/need mouse based head tracking in affected games, you can instead dial the head tracking sensitivity to 0.0 and turn off the gamepad override to use your gamepad natively.