*** This bug is a duplicate of bug 734908 ***
    https://bugs.launchpad.net/bugs/734908

This resets your unity settings but solves the problem:

sudo apt-get install dconf-tools
dconf reset -f /org/compiz/
setsid unity

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https://bugs.launchpad.net/bugs/931460

Title:
  Unity panel displayed on top of full-screen windows

Status in Unity:
  Confirmed
Status in unity package in Ubuntu:
  Confirmed

Bug description:
  This is not a duplicate of bug 591189!

  The issue is  not in appmenu.

  The issue is either in Unity, Compiz, or X11.

  Most likely this issue is with Unity.

  PROBLEM:

  The Unity panel is always visible, even when applications are in full-screen.
  In that case, it is also impossible to interact with the panel; clicks go to 
the full-screen application.

  STEPS TO REPRODUCE:
  1. Install Ubuntu with Unity
  2. Open any kind of application capable of full-screen display
  3. Enter full screen display
  4. Observe that the panel (which includes the application title, the 
application menu, the indicator icons, the clock, and the user and system 
menus) is still visible.
  5. Furthermore observe that this panel cannot be interacted with while the 
full-screen application can.

  DEFINITIONS:

  By "Unity" do not the entire ubuntu experience.
  "Unity" means the user interface plugin for compiz.

  By "full-screen" I do not mean "maximised".
  "Full-screen" means occupying 100% of screen space.

  By "panel" I do not mean "launcher".
  "Panel" means the horizontal bar across the top edge of the screen.

  MORE DETAIL:

  I have an ongoing thread in the forums, but it has been difficult to 
communicate what is going on.
  http://ubuntuforums.org/showthread.php?t=1848739

  I suspect that this bug affects all users of Unity on all platforms,
  but has gone relatively unnoticed due to difficulty communicating the
  issue and the fact that it only affects the upper 14.3% of the screen
  (1cm on my monitor).

  The term "panel" is misinterpreted to apply to both parts of Unity's 
interface although they are a "panel" and a "launcher".
  The terms "full-screen" and "maximised" are misinterpreted as interchangable 
while they are not.
  "Unity" is also misinterpreted as the entire desktop and not one of it's 
components.

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