Pete,
What became of your discussions with LM on this? I'm asking because since upgrading to any versions of 5.1x I am experiencing the strangest behavior in P3d4.1. Sometimes, when I start a scenario, any movement of the mouse in the P3d view temporarily reduces performance to 1-2 FPS. Moving the mouse outside the view (P3d menus, or the Windows taskbar) has no effect. My Saitek X-65F controller is active in FSUIPC 5 and all controllers are disabled in P3d. Once this behavior is encountered during a flight it persists. However, other times when starting a scenario, this behavior is completely absent.
There is nothing of interest (at least to me) in the FSUIPC5 log. Deleting Prepar3d.cfg and letting the sim rebuild it eliminates the issue, until I disable all controllers again in P3d. I tried rebuilding FSUIPC5.ini and that also had no effect. I tried switching between raw input and DirectInput in P3d and that had no effect. It happens whether using either with the default aircraft in the P3d default scenario or with any scenario and any 3rd party aircraft. I even bought a new mouse and this had no effect on the behavior either. It almost seems like either Mouse Look or Mouse Yoke gets permanently enabled in P3d.
Anyway, you can file this away for informational purposes as it may not be related to FSUIPC5 at all.
Jay