I have the same problem with a doubled sound icon (one of two is a 'phantom' 
icon) and a missing network manager icon. Sometimes I have the same problem 
somebody describes here: 
(http://ohioloco.ubuntuforums.org/showthread.php?t=1309227)
like this:" 'In my notification area there's an empty spot at the far right 
without an icon, I have tried moving the notification area, but the empty spot 
stays there, preventing further movement to the right.

Right clicking there and saying "Remove from panel" removes the entire 
notification area. I have removed and added it at an attempt to "restart" the 
area' "
Removing and adding again the notification area solves the problem until next 
reboot.

The difference is that I DON'T HAVE AN 64 bit system. I have 
ubuntu-9.10-desktop-i386 and I sent a report using the commands 
'ubuntu-bug gnome-panel' and 'apport-collect 439448'

-- 
notification area shows wrong icons. erratic behaviour
https://bugs.launchpad.net/bugs/439448
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