Madcatz/Saitek F.L.Y. 9 with X3AP?

[Woodenplank]

I recently picked up a F.L.Y. 9 stick to replace my old and worn out Saitek Cyborg Evo. The stick itself has 2 modes - one where the twist rudder and throttle report as buttons, and one where they report as independent axis. I have the stick set for the second mode.

Windows shows both the twist and the throttle correctly as analog axis. However, X3AP seems to treat the throttle as a button set. Any time the throttle is above the midline, my ship accelerates. It decelerates below the midline. If I set the throttle to the center, I hold speed. Edit to add: The accelerate and decelerate directions on the axis are also the reverse of what they should be, as well as what is shown in Windows. In other words, it's normal in windows, but backwards in game.

Additionally, the twist rudder seems to come and go - sometimes in the middle of a dogfight. One second it's working fine, the next I get nothing.

In both cases, I can alt-tab out of the game and go to the joystick properties in Windows (7 x64) and see both the throttle and the rudder reporting normally.

Any ideas on how I can fix this?