Ive spent days figuring it out, its the game input service API by Microsoft that is the issue (its been an issue since 2013 for alot of games), you need to go into services and disable both GameInput Service and GameInput Redist service, then unplug and re-plug your controller

I have had zero controller issues and more FPS on all games since, disabling these two services has not caused a single issue for me

Goodluck out there my fellow controller divers!