This just affected me as well.  I did nothing more than reboot on my
desktop.  Curious tho, before the startup there was a disktest that
happened before Ubuntu started up , then I noticed my programs, some not
all, were on the right hand side of the panel.  Volume and notifier
stayed put. 2 programs I can quit, the networking status icon stays put
tho. My display is at 1680x1050.

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GNOME Panel icons (on right side) move apparently randomly on session start in 
some situations
https://bugs.launchpad.net/bugs/44082
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