Comment 6 for bug 376528

I'd guess that this is simply yet another one of the https://bugs.launchpad.net/ubuntu/+source/pidgin-libnotify/+bug/589890 bugs

That bug somehow opens up a 'different' message window, that when the user clicks 'close', the window doesn't close.

This bug will likely be fixed when libnotify uses whatever the standard pidgin IM window open method is :)

Don't hold your breath though m8, this bug has been here for almost half a decade...lol