I opened an upstream bug report with Metacity, as the problem seems to be there:
https://bugzilla.gnome.org/show_bug.cgi?id=606431

** Bug watch added: GNOME Bug Tracker #606431
   https://bugzilla.gnome.org/show_bug.cgi?id=606431

** Also affects: metacity via
   https://bugzilla.gnome.org/show_bug.cgi?id=606431
   Importance: Unknown
       Status: Unknown

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GNOME Panel disappears when compositing manager is turned on and eclipse is 
started
https://bugs.launchpad.net/bugs/396590
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