As one can see from the attached screenshot of my panel, I've got a
particularly nasty case of this bug.  As others have noted, it looks to
be tied into changing screen resolutions.  I'm using Feisty.

I play an old video game that needs 640x480.  My display is 1680x1050.
To play the game I wrote a script that calls xrandr before and after the
game to make the necessary adjustments.  That's what started the icons
moving.

Just calling xrandr and playing with different sizes doesn't make the
icons move when I switch back to normal resolution.  It's not at all
clear what needs to happen in addition to changing resolution for the
icons to move.

** Attachment added: "screenshot of mixed up panel"
   http://launchpadlibrarian.net/8076619/icons_gone_crazy.png

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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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