Here: https://bugs.launchpad.net/ubuntu/+source/gnome-utils/+bug/484850 is a 
similar problem with the gnome-dictionary-applet.
Can somebody help to track which is the problematic package? Is it compiz? Why? 
In the clock applet window, how did you know that the problem is with compiz 
and not with the applet?

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shadow remains on desktop after closing clock applet window
https://bugs.launchpad.net/bugs/428783
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