My Logitech/Saitek Pro system with a second Quadrant has gone haywire in this sim. For example: The throttle works perfectly in the Carenado PC-12, Alabeo Waco.
It does not work at all in the A2A J3.
With Majestic q400 the left throttle has only three positions: full idle, mid range, and full power. Right throttle works perfectly.
Other problems include mixture, propeller thrust.

In P3d v3.2 (.3?,.4?) All functions work as they should in every plane.
I have not a clue about what to try next. So far FSUIPC, in sim calibration, reinstalling p3d v4 client, uninstalling/reinstalling all USB connections have not helped.

Can anyone help me with this?
Windows 7 Ultimate OS
New ProFlight system is three months old

If I were you (and this is how i do it) i'd disable the controls in P3D and just use FSUIPC for controls.  Ive noticed if I dont do this sometimes the P3D controls will try to over ride the FSUIPC ones.  Also remember that you can then have separate control bindings for different planes. 

Thanks Kenny

I have tried that once before (quite a while back) with little success. However, tomorrow I will try that first thing. Maybe this time my luck will hold.

There is also a throttle axis calibration utility in the Majestic Q400 control panel. Have you tried that ?