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:
__________________________________________________________________
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.
__________________________________________________________________

Is Unity drawn using override-redirect? Is it mapped with XRaiseWindow?

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https://bugs.launchpad.net/bugs/734908

Title:
  Unity is visible on top of fullscreen apps

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