I am having a similar problem - I think! In FSX, no matter how I work on assigning buttons/axes to a Thrustmaster Warthog throttle and joystick w/ CH pedals, the left and right brakes on the pedals actuate the elevator axis and the aileron axis in addition to their assignments as brakes (for all aircraft - this makes it tough to fly!!). In addition, the trim functions cannot be assigned to what is normally the POV hat. The trim functions used to work as trim in FSX especially with TrackIR working. Is there a way to see what controller assignments are in force using FSUIPC? Would they show up in FSX.cfg? Prior to the re-install, I erased FSX.cfg and re-ran FSX - still no luck.
I have uninstalled and re-installed FSX gold with a clean re-install. The controls used to work just fine in FSX. In fact, they work as they always have in DCSWorld. The clean install should have started a new FSX.cfg - I think.