This is reproducible. Remove the notification area from the top panel
then re-add it and the icons are restored to normal. Reboot and the
error often comes back.

I do not think it is related to video drivers as I see it on two systems
right now, one laptop with Intel video, desktop with nvidia - both do
the same despite different chipsets and drivers.

Effect can be eliminated if the notification area is moved to the another 
panel. On my desktop I moved it to the bottom, on the laptop I use AWN and 
included it there as a widget, in both it now runs perfectly normal.
On either, if I move the notification area back to the default install location 
(top panel, right side) the error returns.

There is a thread on the forums with multiple users reporting the same bug on 
many varied setups.
http://ubuntuforums.org/showthread.php?t=1316676

-- 
[karmic] Certain notification area icons are invisible
https://bugs.launchpad.net/bugs/449910
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