Had this happen upgrading from Ubuntu 10.10 to 11.04 non-Unity 2D GNOME
shell. My problem was Skype was no longer in the tray. Upstream Skype
bug may be found at: https://jira.skype.com/browse/SCL-739

** Also affects: skype
   Importance: Undecided
       Status: New

** Changed in: ubuntu
       Status: New => Confirmed

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https://bugs.launchpad.net/bugs/773307

Title:
  Many apps are missing their tray icons in Natty/Unity

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