The only way I've been able to reproduce this problem is:
1)Launch ArmA 3.
2)Launch TrackIR software.
3)Notice the TrackIR is enabled, but not synced with the game.
One of the solutions is:
1)In ArmA 3, go to the controls menu.
2)Go to peripherals (where the Joystick usually is).
3)Stop and start TrackIR.
The other solution is:
1)In ArmA 3, go to the controls menu.
2)TrackIR should sync with the game at that point.