Not reproducible in Precise.
As far as I know, there were some issues regarding this in Natty from
the Empathy side itself. Are you running Natty?
Empathy 3 fixed most of them I believe.
** Also affects: empathy (Ubuntu)
Importance: Undecided
Status: New
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https://bugs.launchpad.net/bugs/924891
Title:
Empathy launches hidden
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