Funnily enough, this only happens if you launch empathy in Gnome 2, then
run gnome-shell --replace to start Gnome 3. If you quit empathy, then
launch it again in Gnome 3, this problem does not occur.
** Changed in: empathy (Ubuntu)
Status: New => Invalid
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Empathy appears as a window in gnome-shell switcher even when closed
https://bugs.launchpad.net/bugs/647830
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