I found a way to duplicate this issue.

Run the following script in a terminal:
    #!/bin/sh
    sleep 10
    update-manager --no-focus-on-map

Before the update-manager pops up, log into a "Guest Session".  Wait
about 10 seconds, then switch back.  Enter your password at the greeting
screen.  Then you'll see a 'Enter the root password' type of box since
update-manager needs root permissions.  I hit cancel on that window.
Finally, there will be an update-manager icon (the green A with a
progress bar through it)  in the list of program at the left, but it
can't be clicked on to bring it up.  It can be right-clicked to close
it.  Also, alt-tab shows it, but won't switch to it.

Potential pre-requisites:  I'm running on a laptop with an external
monitor.  They are different resolutions.  Also there is an update
available to install.  I'm running Ubuntu 14.04, but I've seen it on
12.04.

Interestingly enough, my "Guest Session" runs on tty F8, meaning that I
can press Ctrl-Alt-F8 and see the guest session.  When I press Ctrl-
Alt-F7 I get my normal session.

I have no clue how to continue looking at this problem.

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https://bugs.launchpad.net/bugs/1003950

Title:
  launcher does not show minimized update manager while clicked

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https://bugs.launchpad.net/compiz/+bug/1003950/+subscriptions

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