Same issue here. It is indeed dissapointing, especially considering that about 90% of TrackIR users are probably people who are using multiple devices, when you consider the kind of games used with TrackIR.
There does seem to be a fairly good solution here:
http://forums.eagle.ru/showthread.php?t=87543
It allows you map the Centre hotkey to pinky paddle short press and the Pause hotkey to pinky paddle long press, without any crossover recognition with the throttle.