according to https://bugs.launchpad.net/bugs/416567, it seems not related to 
empathy.
anyway, even if it's a special behavior of empathy, we should handle this !
could you please post the result of "cairo-dock -l debug" when it happens (only 
the lines between the moment you launch the application and the moment the icon 
should have appeared in the dock).
thanks in advance !

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Cairo-dock always displays empathy contact list in the windows list
https://bugs.launchpad.net/bugs/409821
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