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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You received this bug notification because you are a member of Desktop
Packages, which is subscribed to compiz in Ubuntu.
https://bugs.launchpad.net/bugs/734908

Title:
  Unity is visible on top of fullscreen apps

Status in Ayatana Design:
  Fix Committed
Status in Compiz:
  Triaged
Status in Unity:
  Fix Released
Status in Unity 5.0 series:
  Fix Released
Status in Unity Distro Priority:
  Confirmed
Status in “compiz” package in Ubuntu:
  Confirmed
Status in “unity” package in Ubuntu:
  Fix Released
Status in “compiz” source package in Precise:
  Confirmed
Status in “unity” source package in Precise:
  Fix Released

Bug description:
  [Test Case]
  1. Start a fullscreen application (e.g. Firefox in Fullscreen mode)
     -> Verify that the panel is not visible

  [Regression Potential]
  Visual regressions, shell drawing problems. Part of a big change, many 
regression potentials.

  Original description:

  NOTE: This bug is only about the single monitor case. If you still
  have problems with multiple monitors, see bug 748539 instead.

  ORIGINAL DESCRIPTION:
  In natty alpha 3 up to date, I cannot get fullscreen in any application. 
Panels are still visible.

  Tested with:
  - totem
  - vlc
  - firefox
  - chrome
  - geany

  Unity panel and top bar are always on top.

  -----------------------------------------------------
  Desired Solution:

  - When a window is fullscreen (note: this should not be confused with
  the *maximised* state) the menu bar should not be displayed.

To manage notifications about this bug go to:
https://bugs.launchpad.net/ayatana-design/+bug/734908/+subscriptions

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