ilpillo:

I deleted .gconf/apps/panel and at first the problem went away, but when
I added back all of my applets the problem came back. This seems to
reinforce the hypothesis that the problem is due to load time. The
applets I'm currently using are:

Quit...
Clock
Volume Control
User Switcher
Keyboard Indicator
Search for Files...
Timer
Deskbar
Tomboy Notes

Tomboy in particular takes ages to load, so it might be why this happens
so often for me, but it has happened even without Tomboy. I have seen it
happen with just the following set:

Quit...
Clock
Volume Control
User Switcher
Keyboard Indicator
Timer

-- 
System tray loads with all non-applet icons "popped out" into windows
https://bugs.launchpad.net/bugs/223418
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