Ok, so I originally dealt with this issue and gave up. Prepar3d v2 had just been released and I couldn't really get any help.
I have a logitech attack, had it for years. Works perfectly fine on FSX. All my drivers are updated and I have the latest FSUIPC add on for Prepar installed.
If I load up prepar3d on the default Norfolk runway and use the default Bonanza the joystick has no control of taxiing, the aircraft just goes in circles, the throttle seems to work and does the brakes button. If I load my Carenado Commander 114 sometimes it will work correctly, not always, sometimes. While running a flight if I go into the controls config, when I exit out it just stops working all together, no throttles, no nothing.
Very weird and this was a problem day one. I have since completely reinstalled my OS and Both FSX and Prepar3d.
Basically Prepar3d is useless to me unless I can resolve this.. Any ideas?