When you go to OPTIONS > CONTROLLERS > Map Controllers, is your Saitek selected in the upper right corner dropdown box?
Also, is the correct *Mode* selected and is it mapped? You need to have at least mode1 (planes) and mode2 (Vehicles) mapped and either buttons to switch manually mapped or the box "auto selection of mode..." checked.
Another thing that happens with my X45 at times is... it just doesnt work (no lights on the buttons either). What i need to do then is simply plug it out and back in - then restart AH.
Try backing up your Settings folder (HTC/Aces High II/Settings) - then delete it in the game installment. (The settings get not deleted by an uninstall!) Restart the game and check if the problem persists - if not, try to copy your settings back in 1 by 1 (first the headposition files, then the radio, video cfgs etc etc) - make sure if the stick still works after every file you copy in. Last for the jsm (=joystick config) files. That way you can find the "culprit" in your settings.
If the problem still persists with default settings.... ill have to think hard again

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