My biggest problem initially with TrackIR was that, if it lost sight of the dots (or reference marks, or whatever you want to call them), the view snapped to some default instead of staying where it was at the point of losing the dots.
For me, it made looking "back and up" a problem, as it would go to where it should, then if I tilted my head back too far, the view would snap to something else completely. It was very annoying.
I'll try things with the suggested setup here and see if that helps.
I wish the film viewer would allow use of TrackIR -- it would be so much easier to make nice movies.