I am seeing this also. Recently upgraded from Jaunty to Karmic and while I had no issues with gnome-do in Jaunty I am now seeing a grey rectangular box appear in the upper left'ish corner of the screen before the proper gnome-do window appears centered on my screen. Note that this happens very quickly and all you see is the ghost image of that grey rectangular window.
I am seeing this also. Recently upgraded from Jaunty to Karmic and while I had no issues with gnome-do in Jaunty I am now seeing a grey rectangular box appear in the upper left'ish corner of the screen before the proper gnome-do window appears centered on my screen. Note that this happens very quickly and all you see is the ghost image of that grey rectangular window.