There are a few different bug filings for this problem. From reading
through them, it may be related to nVidia, as the only reported video
cards have been nVidia. I have an nVidia 8600 with the proprietary
driver and a dual display setup, and I'm running 64 bit Ubuntu.

Switching between virtual desktops seems to get rid of the shadow
easily.

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GKSudo dialogue leaves drop shadow even when closed
https://bugs.launchpad.net/bugs/219477
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