This is a typical effect of a mouse driver. I don't use any except what windows provides and if a mouse doesn't work with windows, then I exchange it.
Hint: Don't install mouse drivers.
Whenever I have a window in focus (none in specific, but it does 'lock' to one over time), my mouse slows down to 50%. When I move my mouse to another window, however, it speeds back up. I have no idea what's causing this.