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Binary package hint: compiz
On Natty, if any application in fullscreen mode opens a new window, then the Unity panel and launcher will come to the foreground on top of the fullscreen view. To see this, open gedit, choose View->Fullscreen, then press Ctrl+F for Find. As the Find dialog appears, the Unity panel and launcher will appear too.
I've also observed this behavior in Gimp and Shotwell. It probably occurs in other applications too.
This also happens when logged into the classic desktop: there, the gnome-panels come to the foreground. It does not, however, happen when running Metacity instead of Compiz in the classic desktop. So it apppears that the behavior is related to Compiz.