Had a similar issue, and it seemed to be caused by the game losing focus from Windows 10. Gamepad would stop working, and framerate would drop to 15 fps and stay there, even when alt-tabbing back into the game.

I unchecked the options in system config that is something along the lines of "limit frame rate when not active window" and it fixed the issue. There's also a setting in there to keep registering the gamepad when not active window.