I would check to make sure that something is not actively jumping as the top active window. It sounds like another program started up, but stayed in the background, such as the xbox thing that LalaRu mentioned. I have happened in the past where this very thing caused my game fps to drop, yet the mouse and keyboard was working for the game.

If you really cannot find out what it is, there is a setting where you disable the limit frame rate while the game is not active. It is on by default. I know this is not a solution, but it is a possible band-aid till the root caused is figured out.