In case it is relevant, I should add that I typically run both Synaptic
and update-manager from a gnome-terminal using sudo.

** Description changed:

  To reproduce:
  
  1. Run Firefox.
- 2. Run Synaptic (non-maximized) and select a program to install or to 
reinstall. 
+ 2. Run Synaptic (non-maximized) and select a program to install or to 
reinstall.
  3. Click Apply and OK to install/reinstall the program and then while 
Synaptic is downloading, click on Firefox to bring the Firefox window to the 
front.
  4. When Synaptic finishes downloading and starts installing, it brings its 
window and dialog back to the front, ie in front of Firefox's window.
  5. Click on either the part of the Firefox window visible behind Synaptic or 
on the Firefox icon in unity-launcher to try and restore to the front.
  
  Result: nothing happens. Unity does not bring Firefox's window back to
  the front, presumably because unity still thinks Firefox is the current
  application/front window.
  
  The only workaround I've found is to click on the Synaptic window or its
  unity-launcher icon and then to click on Firefox to bring it back to the
  front.
  
+ 
+ A second way of reproducing this, if there is a system update for which the 
list of changes is not yet available, is:
+ 
+ 1. Run Firefox and minimize it.
+ 2. Run update-manager and find an update that has an http link for the 
updates, ie where it says "The list of changes is not available yet. Please 
use...".
+ 3. Click on the link. Firefox will be brought to the front, obscuring 
update-manager, but unity-launcher will have a blue arrow next to Firefox's 
icon to indicate that it needs attention.
+ 4. Click on update-manager's icon in unity-launcher to bring it back to the 
front.
+ 
+ Result: nothing happens. Unity thinks update-manager is already the front 
window.
+  
+ 
+ 
  ProblemType: Bug
  DistroRelease: Ubuntu 11.04
  Package: unity 3.8.16-0ubuntu1~natty1
  Uname: Linux 3.0.0-rc5-git-20110628.1119 x86_64
  Architecture: amd64
  CompizPlugins: 
[core,bailer,detection,composite,opengl,imgjpeg,decor,vpswitch,text,place,move,mousepoll,regex,compiztoolbox,snap,session,gnomecompat,resize,wall,imgpng,grid,animation,unitymtgrabhandles,expo,ezoom,staticswitcher,workarounds,fade,scale,scaleaddon,unityshell]
  Date: Tue Jun 28 12:56:19 2011
  InstallationMedia: Ubuntu 11.04 "Natty Narwhal" - Beta amd64 (20110330)
  ProcEnviron:
-  LANGUAGE=en_US:en
-  LANG=en_US.UTF-8
-  SHELL=/bin/bash
+  LANGUAGE=en_US:en
+  LANG=en_US.UTF-8
+  SHELL=/bin/bash
  SourcePackage: unity
  UpgradeStatus: No upgrade log present (probably fresh install)

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https://bugs.launchpad.net/bugs/802816

Title:
  unity doesn't realise when applications bring their windows to the
  front

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