Skyrim and other games only allow either mouse (required for vorpX’s head tracking) or gamepad, hence the gamepad is auto-disabled by vorpX.
vorpX has a built in gamepad emulation for these games (a bare bones version of tools like Xpadder or Pinnacle Profiler), which you can freely configure in the vorpX ingame menu. To do that go to the “Gamepad” page of the ingame menu and press the “Button Mappings” button.
For Skyrim and various other games there will be a new solution for this issue soon. With the next vorpX version you will be able to use your gamepad natively in Skyrim.