After installing Windows 10 Update KB3140743 I noticed a massive performance hit with Retroarch. Everything on my system was running perfectly before this update and after was running around 20 frames per second slower and basically impossible to play. I don’t know what exactly in the update caused this issue but uninstalling this specific update everything was perfect again. This was only a problem within Retroarch, other standalone programs and emulators did not seem to be affected by this update as far as I could tell.
It didn’t hurt RetroArch performance on my system. I know that update causes issues with the Xbox One controller with some games and stand alone Dosbox. I’ve only tested and confirmed it causing GTA V to crash so far. There’s supposed to be some beeping and mouse cursor jittering when you plug or unplug the controller; maybe that is causing your performance issue? I think if you use it wirelessly, turning it on or off will cause the same problem. I use mine wired and don’t ever unplug it, so I haven’t had that issue yet.