This can happen for example on Flash website, like YouTube.

$ ps aux | grep firefox
foobar  6630  3.6  2.0 198764 70408 ?        Sl   13:27   0:06 
/usr/lib/firefox-3.0b5/firefox
foobar  6721  7.7  0.8  93496 29548 ?        Sl   13:30   0:00 
/usr/lib/firefox-3.0b5/firefox
foobar  6728  0.0  0.0   3008   768 pts/0    R+   13:30   0:00 grep firefox

Then I click on the OK button on the "Firefox is already running, but is
not responding. To open a new window, you must first close the existing
Firefox process, or restart your system." dialog.

$ ps aux | grep firefox
foobar  6630  3.3  2.0 198764 70408 ?        Sl   13:27   0:06 
/usr/lib/firefox-3.0b5/firefox
foobar  6732  0.0  0.0   3008   772 pts/0    R+   13:31   0:00 grep firefox

So this means Firefox is running in the background even if I close it...

-- 
Firefox is already running, but is not responding...
https://bugs.launchpad.net/bugs/232005
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