Ok, I tested it with other themes: human, ashes, oransun, and others - so it's 
probably gnome-panel bug.
Different icons dissappear, not all, mostly single ones, or 2.
Ie. opera's, gajim's, ooquicklaunch, network-manager...
BTW: I'm returning my laptop from sleep frequently - I don't know if it has to 
do anything with it.
I can attach my .xsession-errors but it doesn't include anything useful IMO. I 
have GTK-dbg installed.

** Attachment added: "my xsessions-errors file"
   http://launchpadlibrarian.net/8314972/.xsession-errors

-- 
icons in gnome tray disappear
https://bugs.launchpad.net/bugs/123390
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