Well, although I have not gotten a 100% solid confirm that this problem exists, I will post the fixes. MCG_Rattlesnake has posted that it is confirmed by beta testers to be an issue and the patch will be out soon to fix it.
So, that being said, I would assume, although I have not confirmed it myself in the final version, thet this exists.
When you press the center button for the TrackIR, the view auto centers to the lower instrument panel. On one computer, it will center dirctly between the pilots knees. On another computer, it centers on the pilots left knee. So, it seems to either be system dependant or on some other factor.
Two ways to fix this.
1. Center the TrackIR. Where ever it centers to, look at that spot with your head and center it again. When you look back to center with your head, your view will follow and will be reasonably close. You will have to play with it a bit to make it work perfectly.
2. Center the TrackIR when you are looking straight ahead where your center head position is and then, WITHOUT MOVING YOUR HEAD, quickly hit the pause button to pause the TrackIR. Then use your POV hat to center your view where you want it. Then, unpause the TrackIR and go about blowing stuff up.
Lets hope that the problem doesn't exist, but if it does, here are the fixes until an official patch is released.