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[BlueCase <1235814@xxxxxxxxxxxxxxxxxx>]

Exactly the same here with 13.04 and 13.10.
Seems to be compiz related.

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https://bugs.launchpad.net/bugs/1235814

Title:
  indicator-messages fails to bring application windows to foreground

Status in “indicator-messages” package in Ubuntu:
  Confirmed

Bug description:
  When using Thunderbird and pidgin (only apps I have tried so far), the
  message indicator displays a new message available, but when selecting
  the message, instead of foregrounding the window containing the
  message, it just wiggles the launcher entry, and leaves it hidden,
  until I manually click the launcher icon to bring it to the front.  If
  it is required, I can provide a screencast to demonstrate.

  ProblemType: Bug
  DistroRelease: Ubuntu 13.04
  Package: indicator-messages 12.10.6daily13.04.09-0ubuntu1
  ProcVersionSignature: Ubuntu 3.8.0-31.46-generic 3.8.13.8
  Uname: Linux 3.8.0-31-generic x86_64
  ApportVersion: 2.9.2-0ubuntu8.3
  Architecture: amd64
  Date: Sat Oct  5 19:28:31 2013
  InstallationDate: Installed on 2013-10-05 (0 days ago)
  InstallationMedia: Ubuntu 13.04 "Raring Ringtail" - Release amd64 (20130424)
  MarkForUpload: True
  ProcEnviron:
   TERM=xterm
   PATH=(custom, no user)
   XDG_RUNTIME_DIR=<set>
   LANG=en_US.UTF-8
   SHELL=/bin/bash
  SourcePackage: indicator-messages
  UpgradeStatus: No upgrade log present (probably fresh install)

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