PB strives to be quite uncontrollable once it will be minimized somehow or by another application because it will be then with a windowed sized. Bounding boxes will be then different and probably mostly outside of the game boundaries.
I know that it maybe something to do with Steam and may be difficult to fix. This is why I didn't post this to a bug and glitches forums. Keyboard shortcut would allow to switch from full screen to windowed mode and back which should again show full screen properly without forcing PB to shut down first.