I know this has already been mentioned several times, but making sure I was running Track IR & ARMA2 "administrator mode" fixed my problems.
I'm not 100% happy with it yet though... my head is moving around way too much in infantry mode which is making aiming really awkward. I'm tweaking my Track IR profile to see if I can make a suitable setup - I need a bigger dead zone or something. I have also noticed that my head (in game) will sometimes get stuck if I turn it too far - recentering using F12 fixes it, so I'm sure it is a Track IR issue and not ARMA2.
Anyway, if anyone is using a custom profile for ARMA2 I would love to see a screenshot of your "Gauges". The default ones just arent working out for me.