Happens in Xubuntu 12.04 whenever an auto-update is available. Icon &
notification bubble appear, display for about 20 - 30 seconds then
disappear. After about 5 minutes, icon & notification reappear then
notification times out leaving icon in taskbar.

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https://bugs.launchpad.net/bugs/1061469

Title:
  Update icon and notification disappear after a few seconds when
  updates are downloaded automatically

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