I can confirm the issue being related to something empathy does, in particular 
I noticed it happening when resuming from suspend: 
- I get some automated messages from nickserv and channel bots, the icons 
indicates two messages per channel
- if I right click on the icon and select "remove", another "ping" sound is 
played, the second message pops up from the tray and the tray disappear.

Sometimes I had an even stranger behaviour: by doing the above actions
while in overview mode, notification area moved up to about 1/4 of the
screen, like if the pop up animation was triggered again while the bar
was already visible.

I'm using Ubuntu 12.10 with -proposed repository enabled.

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https://bugs.launchpad.net/bugs/1067265

Title:
  gnome-shell (3.6) notification bar disappears

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