this bug has become worse for me since upgrading to lucid. i had the
problem with previous versions of ubuntu but after resetting the
positions a few times gnome seemed to "learn". The problem is not
related to rebooting or restarting x or anything like that. the problem
is that at home i connect a big lcd monitor to my laptop via a vga
cable, and when away obviously i just use the laptop screen. on changing
from one to the other the applets are all in the wrong order, or
floating in space.

im using the proprietary Nvidia driver, although in my opinion the
problem is not related to that. i see the fix as being achieved by
having the actual order of the applets saved, not just the positions.
any space should be saved, as well as noting when applets are touching,
or when an applet touches the end of the panel. when applets are
touching each other or the edge they will remain stuck together or to
the edge, with the space being dynamically altered. floating applets
would be a special case, and are detected by noting that nothing is
stuck to either side except space.

i realise this is probably far from the logic currently used to
determine the locations, but i would point out that what i have
suggested is very similar to the way the window controls are positioned
on any gnome window. to see the way this is set up open gconf-editor and
go to Apps -> Metacity -> General" and choose the  key named
"button_layout".

by the way, if like me you hate the new lucid window control layout see
this link:

http://hubpages.com/hub/Move-Window-Controls-back-to-right-in-
Ubuntu-1004

kind regards

-- 
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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