I've seen something similar but I'm not sure if it's the same.
On my laptop I run mostly pidgin (irc etc) and occasionally firefox, and 
sometimes if I kill the firefox with alt-f4 or clicking on the close one of the 
irc windows will go.

Dave

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When closing application, not always the application with the focus is closed
https://bugs.launchpad.net/bugs/612304
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