Sounds like AH is confused as to the assignment of your controllers. I have the X36 USB Combo and CH Usb Pro Pedals. On bootup, Windows assigns Controller 1 to the pedals, and controller 2 to the X36.
If I don;t reset this before starting AH I've noticed that my rudders control my throttle, left pedal controls elevators etc.
Check your joystick assignments and THEN reset your axes from the AH joystick control panel.
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=357th Pony Express=
Aces High Training Corps