I have this issue since updating from Lucid to Precise. Even switched to Pidgin because of this. I have no realy clue why it happens, but it seems to be related to multiple open empathy windows on multiple desktops and then receiving a message from somebody where you have already a window open on another screen. Then it never opens a new window (if i press the indicator), nor it switches the desktop to the window. When i mange to find the window manually, i only see it empty.
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