I haven't been able to reproduce this reliably, but what happens is
this.

1. I'm working on something, usually in a maximized window, 
2. a notification from empathy pops up,
3. I move the mouse cursor to the left edge of the screen, wait for the dash to 
appear and switch to empathy clicking on its icon

My guess is that this happens when I move the mouse cursor away from the
dash before it disappears again. Another factor that may contribute to
this is that I usually run empathy in a different virtual desktop. I'm
sure it never happens if I switch to empathy using the alt-tab shortcut.

I suspect this is related to #885941 since the steps above trigger weird
half-focus issues in other applications as well, e.g.

* I can type in gnome-terminal but the title bar is in the inactive state and 
the terminal cursor is the hollow one
* If I switch to firefox the awesome bar popup doesnt' work anymore and right 
click menus disappear as soon as I move the mouse (see 
http://support.mozilla.com/en-US/questions/890796)
* If I switch to eclipse the gui is functional (I can scroll, I can switch 
between editor tabs...) but I can't type

When any of the above happens a quick switch to another app and back
using the alt-tab shortcut fixes it.

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https://bugs.launchpad.net/bugs/887025

Title:
  Empathy message notifications appear even if empathy has focus

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