Another update:

Sometimes it occurs even without having to be logged in (from a
terminal) as root. Or, if you think this is a non-standard thing to do,
try logging in as another standard user on the machine (su -l
another_user).

** Description changed:

  Binary package hint: unity
  
  If I move a non-pinned icon for a running application to the middle of
  the Unity Bar (middle = having applications above and below it) and then
  I minimize and restore this application, the icon will be moved to the
  bottom of the Unity Bar. This makes it confusing as users usually
  arrange their icons and expect them to keep their positions unchanged.
  
  UPDATE (steps to reproduce):
  
  Using this, it will always happen for me:
  
  * Close all programs that have icons in the Unity Bar
  
  * Unpin all programs so that the Bar will be empty (except for those
  built-in items that you can't remove)
  
  * Start Transmission
  
  * Start Banshee
  
  * Minimize Banshee
  
  * Minimize Transmission
  
  * Now move the Banshee icon so that it will be above Transmission's icon
  in the Unity Bar
  
  * Now click on the desktop (anywhere in an empty spot)
  
  * Click on the Banshee icon
  
  Expected result: Banshee should keep its top position in the Unity Bar
  
  What actually happens: Banshee will be moved below Transmission
  
  UPDATE 2:
  
  It might only happen when the root user is logged in (not graphically,
  just in a terminal running under the normal user). When trying the above
  steps, I was logged in as root (su -l root) in a non-attached tmux
  session (root account enabled with sudo passwd -l root). Being logged in
  as root has been for a long time causing problems like not being able to
  restart (results in being logged out instead of restarting the computer
  if the root user was logged in in some terminal, at the moment of
  restart). This one... is way stranger though. (Why was I logged in as
  root - in a terminal? Because sometimes, when performing many
  administrative tasks it's easier than typing sudo in front of all
  commands).
+ 
+ UPDATE 3:
+ 
+ Sometimes it occurs even without having to be logged in (from a
+ terminal) as root. Or, if you think this is a non-standard thing to do,
+ try logging in as another standard user on the machine (su -l
+ another_user).

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https://bugs.launchpad.net/bugs/773762

Title:
  Non-pinned icons for running applications will not maintain their
  position in the Unity Bar

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