I just got AFP with the commander last week. It's great.

The commander has the hardware in Mode 2 (rachet on throttle - left gimbal up/down), but transmits the signal to the PC with the throttle as the elevator, and vice-versa. This is no problem in AFP, as you can assign any of the "joystick" channels to any axis control. However, this may limit the use of the commander in any other sim, such as Microsoft Flight Simulater. Would have been nicer if the throttle (left gimbal up/down) showed up in Windows as the throttle. When I first attached the Commander to my PC, and saw that the throttle, and elevator were reversed, in the Windows calibration area, I considered rewiring the controller, but when I fired up AFP, and saw how easy it is to assign the channels, I didn't bother.