I tried it a few times and each time it only worked when I clicked on the desktop.
So the script won't run unless you click to the Finder first, then it still leaves one app open?
Not sure why it won't quit all. I just tried on another machine and quit all quits all. You're not running any anti-virus, MacKeeper, or any other useless clean my Mac product are you? You're on Mountain Lion? I tried from Snow Leopard and Mountain Lion.
Well at least it's most of the way there, only one app to quit then.
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