Was just able to confirm this on Jaunty (i686) using:

sleep 10; xmessage Hello

Then locking the screen.   After ten seconds, the panels emerge from the
darkness.

Using compiz on Intel 915GM, so it's not just an ATI issue.

-- 
Top and Bottom panels show up on a Locked Ubuntu Screen when a window pops up 
(e.g. Updates/aMSN chat window)
https://bugs.launchpad.net/bugs/396411
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