One way to solve this problem that has worked for me:
Instead of running compiz by putting it into /home/<user>/.kde/Autostart, add a
new file called /usr/share/autostart/compiz.desktop (see attachment)
Then edit the file /usr/share/autostart/panel.desktop: You need to change the
line
X-KDE-autostart-after=kdesktop
to read
X-KDE-autostart-after=compiz
This should run compiz before running any application with a tray icon,
thus ensuring that all trayicons are there.
** Attachment added: "compiz.desktop"
http://launchpadlibrarian.net/10683409/compiz.desktop
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Missing Icons in system tray when Compiz is used...
https://bugs.launchpad.net/bugs/111232
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