I also have this bug in the release version of Karmic.

This bug occurs on every startup. Certain apps just refuse to show up in
the notification area. Most importantly, Thunderbird and Pidgin. This is
very annoying as I can't tell when someone has sent me an IM or an
email!! Empathy and emesene show up fine.

I am not using compiz. I will attach my xorg.conf.

I have tried the following workarounds:
1. Closing the app then reopening it. No change.
2. Removing the notification panel then re-adding. No change.
3. Swapping to different themes and icon sets. No change.
4. In pidgin, I toggled the notification icon off then on. The icon flashed up 
in the notification area for an instant, then disappeared.

I upgraded my system from Jaunty, which gave me no notification bugs.

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