Some users have reported TrackIR no longer working in Lock-On: Flaming Cliffs, with the latest game patch (1.12a).
To remedy this simply open your LOMAC->Input folder, and delete the TrackIR.ini file; then go to LOMAC->Config folder, and delete the TrackIR.ini file located here as well.
http://www.naturalpoint.com/trackir/03-enhanced-games/game-lock-on-11-flaming-cliffs.html