I've submitted the bug upstream with a possible patch to fix it.  I believe 
that this bug is related to metacity's focus-stealing prevention and use of 
stale X11 timestamps to activate windows.  Please see the upstream bug for more 
details:
https://bugzilla.gnome.org/show_bug.cgi?id=676076

** Bug watch added: GNOME Bug Tracker #676076
   https://bugzilla.gnome.org/show_bug.cgi?id=676076

** Also affects: policykit-gnome via
   https://bugzilla.gnome.org/show_bug.cgi?id=676076
   Importance: Unknown
       Status: Unknown

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https://bugs.launchpad.net/bugs/946171

Title:
  Authentication dialog window loses focus easily - Ubuntu 12.04

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