That's odd that you can't set it. I plugged my TrackIR in, started AH without VR and the gunsight was slightly low. I pressed my "tracker center" button and the gunsight was centered in the glass. I took off the headset and the gunsight was still centered in the glass.
If you need to restore defaults just delete the P38L hps file.
Easy, quick test. Follow these steps:
Start the game with TrackIR
Pause TrackIR (F9 is default button)
Move the head position up a bit, 1/4" should be enough.
Hit F10 to save position.
Unpause TrackIR (F9 is default button)
What happens on my machine is, the head position jumps up a bit. If you keep TrackIR enabled and hit F10, every time you do it the head position will jump up a bit more. Makes it tricky to get your head just where you want it.
It doesn't have anything to do with TrackIR losing center, it's where the game is recording the center position of the head.
Wiley.