On Ubuntu Jaunty, this is fixed.
Logout causes the "do you want to save" dialog to pop up on the current virtual 
desktop. Additionally, the panel stays responsive and the "some applications 
are blocking logout" dialog is displayed.

** Changed in: gedit (Ubuntu)
       Status: Triaged => Fix Released

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Not obvious when logout is stalled by window on another virtual desktop / 
window beneath front-most one / window is minimised
https://bugs.launchpad.net/bugs/33673
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