Double check to see you don't have multiple functions mapped to the same keys/axis. Especially if you have stuff mapped under "chat", "comms", or "views". Sometimes, things work with the mouse pointer on screen, and not when its off, and therefore, can be causing one control setting to take precedent over another.
Do you have something set for panning views, and while in that mode, its disabling your throttle/pitch?
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i7-920 @ 4.1Ghz
Gigabyte GA-X58A-UD3R
12 GB DDR3 1600 RAM
GTX 560Ti with 2GB (latest beta driver)
22" monitor @ 1680x1050
TrackIR 5
Saitek X52
Saitek pedals
Win7 64-bit Ultimate
"Ignorance speaks loudly, so as to be heard; but its volume proves reason to doubt every word."~Wes Fessler
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