The "program is still running. shut down anyway" dialog appears to me too, but 
only after using Firefox. When I don't open FF at all in a session, I don't get 
the dialog either. 
Sometimes when I close FF and try to reopen it, I get a message that 
firefox-bin is still running, and my cursor is busy, so I have to wait for the 
browser to close properly before restarting it. Obviously I'm just guessing, 
but something like that must be going on with the shut down situation. When I'm 
shutting down fast after closing FF, I sometimes get the dialog and sometimes 
don't, but I surely don't get it when I wait a little after closing the browser 
and only then inititiate a shut down.

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https://bugs.launchpad.net/bugs/313228

Title:
  a program is still running but i want shut down anyway

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