The problem occurs on Xchat 2.8.8 on Ubuntu 11.10 with Gnome3 (Gnome shell) .
Notifications (e.g. when I'm directly adressed in a message) pop up in the system tray (bottom right) and do not disappear. You have to manually close every single xchat icon down there.
Someone already tried to patch it, but the patch isn't current anymore: http://mightaswellhackit.wordpress.com/2011/05/07/xchat-notifications-on-gnome-3/
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