I'm having this problem, too using:

Kubuntu Gutsy 32 bit (updated daily)
Nvidia 8600 GT (restricted manager Nvidia driver)
Compiz 1:0.5.2+git20070918-0ubuntu5

Mainly with adept notifier and Kcheckgmail, but occasionally also with
Amarok. The systray icons just appear in the top right corner of the
workspace instead of the system tray. If you can close them they reopen
in the correct place, but this isn't alsways possible.

-- 
starting compiz in KDE displaces adept from tray
https://bugs.launchpad.net/bugs/131013
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