@mac_v: Thanks for the offer, I don't think I need any extra debugging
information or logs, I can easily reproduce this problem on my laptop by
plugging in an external display with a different resolution. Actually
anything that resizes the desktop (Fn+F7 on my laptop) will trigger the
problem. (Sometimes it requires logging out, but often it's immediate) I
believe a patch in gnome-bugs #341441 point in the right direction, this
is a problem of the GConf position data for the panel items getting
changed when they shouldn't, and the items move. I'm looking at updating
the patch attached to the upstream bug to the latest code. I've just
moved, so my development machine is packed in a box this week, I'll get
back to this bug over the weekend.

For all of the fans of this bug, here's my summary of problem:
It seems the "panel_right_stick" applet setting is getting cleared. For 
example, in GConf "/apps/panel/applets/trashapplet_screen0/panel_right_stick" 
is "true" before switching desktops (with Fn+F7, or plugging in a screen, etc), 
and "false" afterwards. The applet "position" is measured from the left panel 
edge, but "panel_right_stick" switches this to the right/bottom edge. However, 
"position" still measures the distance to the left edge *of the applet*. The 
default Ubuntu Trash applet, in the bottom right corner, position is 26 for 
instance, instead of 0. Once this setting goes awry you will even see negative 
values and the like. For example, my FastUserSwitchApplet (in the top right 
corner) currently indicates a position of "-152" instead of 0 (or however many 
pixels wide it is to the left edge of the applet). And to top that all off, 
sometimes applets (like Clock) don't seem to set the "panel_right_stick" to 
true when they should.

-- 
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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