Hmm, I just had an idea that might do the trick, if you
really want those messages to not show.
Unfortunatly, that idea would require some knowledge of scripting (read: programming) as well as some (basic) knowledge of the windows interiors (read: software architecture).
You could download a copy of a program called "Autohotkey". It features a quite powerful scripting interface. In fact, powerful enough, to manipulate specific windows.
Baseline:
If you know what HWND is, you've got a chance to get rid of the popup messages.
If not, hone your "mouse click on little X-buttons" skills