Comment 135 for bug 734908

Have I mentioned before that I think this is a layering problem?

I was reading the old xscreensaver (one of many things unity appears on top of) faq and came a across this:
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Every few minutes, xscreensaver will raise itself above any other windows that have popped up, but it can't prevent other programs from popping up their windows in the first place. So they will appear for a little while, and then be hidden.

If this is happening and it bothers you, switching to a different window manager may fix it.

You might consider this a bug in your window manager (though some consider it a feature.) If you think it's a bug, then the magic incantation to repeat to the author of your window manager is as follows: "you should be mapping windows with XRestackWindows instead of XRaiseWindow, to ensure that managed windows always appear below override-redirect windows."

It is also possible that the application that is popping up the window is doing so using an override-redirect window of its own. (This is currently the case with GTK_WINDOW_POPUP style dialogs.) In that case, it is impossible for either xscreensaver or the window manager to prevent those windows from popping up, since override-redirect windows, by definition, bypass the window manager.
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Is Unity drawn using override-redirect? Is it mapped with XRaiseWindow?