much appreciated!
It also may be a multimonitor issue. Even if its not the "Active" window, it is the topmost window when I was testing it, on the monitor it was on, even though my active window was the game I was playing.
Edit: Actually it no longer seems to be happening? I have no idea what that was.
Edit2: Okay after testing some more, it does it if you have pressed any buttons on it, then controller input becomes enabled somehow. It swaps presets and also navigates through its menus.