Did you find a fix? I have a .jsm file I can give you.
I have a similar problem, but only after flying in Warbirds. It was fine in Aces High in the beginning, but now my Saitek Rudder pedals will not center. The ball moves off to the right (left rudder), the elevator goes up, the airleron rolls slightly to the right. I can fly by applying pressure to counterbalance, or I can turn on Combat Trim. Turning on Combat trim seems to help, but clearly this set up is not working normally.
I did reinstall the drivers, and calibrated joystick inflight as well as looking at the x y z values
Any X52 Pro and pedal users out there?