I don't think it was fixed. I still have it with empathy 2.28.1.
Here is a video showing the current behaviour in fully up-to-date
karmic.
** Changed in: empathy (Ubuntu)
Status: Fix Released => Confirmed
** Attachment added: "out.ogv"
http://launchpadlibrarian.net/34423544/out.ogv
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when Empathy is opened from Message Indicator, it appears below current window
https://bugs.launchpad.net/bugs/392153
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