Thanks for your bugreport.
The current version of update-notifier in gutsy uses a GtkStatusIcon now
instead of the old EggTrayIcon. This means that this problem should be
fixed now. Please reopen if you still experience it with gutsy.
thanks,
Michael
** Changed in: update-notifier (Ubuntu)
Status: Confirmed => Fix Released
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Icon in the notification area is not always transparent
https://bugs.launchpad.net/bugs/46203
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