What video card and driver are you using?  Are you using 32 or 64 bit
Ubuntu?  Does this happen on all screen edges and with floating panels
or only in certain positions?  IMaybe the graphics card isn't properly
redrawing the part of the screen into which the panel is being placed?

I can't reproduce this problem using Compiz, 32bit Hardy, and fglrx.

** Changed in: gnome-panel (Ubuntu)
       Status: New => Incomplete

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Gnome panel bugs with secondary monitor
https://bugs.launchpad.net/bugs/271343
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