There might be a workaround.
I experienced that when you drag the popup balloon to a screen that is later removed, the popup balloons appear on that location still even when the screen is no longer attached.
So the workaround involves attaching and detaching another screen, which is not ideal :-), but maybe it can be a temporary solution while you wait for software changes.
If you go for this workaround I also advise to set the auto-hide feature suggested by Matthias.