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Wireless 360 Pad Mod to FightStick Issues

Stuck

Mid Tier Whore. 1 combo and a dream.
OK my friend has modded three wireless Xbox 360 controllers to fightsticks. They all work perfect in other fighting games. However in MK9, you can't neutral jump or neutral crouch. What's weird is that the stick moves up and down fine in the menus and when jumping up/forward, up/back, down/forward, down/back. All of the buttons are modded except the RT and LT because they are analog. The sticks are not modded either. The stick works off of the d-pad. Anyone that could help would be appreciated.