I know this sounds kinda basic, but sometimes the answer to a problem is something very simple and basic. Have you gone into Aces High Setup/joystick/choose joystick and assigned each axis for your sticks and pedals to the correct stick, and the correct input?
If your stick responds in Windows, and then not in the game, it does sound like you may not have assigned a function to each axis.
Be sure to hit enable, or whatever, after assigning each stick and axis, then make sure to hit apply and ok to save out. Check it out in the calibration area.
Hope it's as simple as that.
Ranger Bob