Hi,
I'm using Ubuntu Jaunty and have the same problem for as far as i remember 
using gnome :( (from dapper i think).
My settings is the two pannels at the top. 

Until Jaunty it was not so problematic as i could drag and drop one
panel to the bottom and to the top really easily at startup. But since
Jaunty i just can't drag and drop panels any more (if someone know how
to enable drag&drop again i'm interested in) and must right click and
then click properties and then configure the pannel to bottom then to
top and then close the window. This is just awfull to loose all that
time at every gnome login.

But looking around i found first the script in that topic and then
another at http://forum.ubuntu-fr.org/viewtopic.php?pid=2683139 but none
really work for me :(. So playing arround with gconf-eidtor i finally
find a setting that seems to work for 2 weeks now on the 2 computers i
use every day.

So in gconf-editor go to apps->panel ->general and find the
corresponding entry for you in my case toplevel_id_list and reorder the
panels in the list in the order you want them to appear in this case the
first is at the edge of the screen.

If you don't know which id match one or another panel then you can go to
( alway sin gconf-editor ) apps->panel->toplevels there you will finds
your panels and playing with the option enable_buttons for example may
help you identify each of your panels.

Hope this will be a definitive solution, and that i will help others,
Best regards to all.

-- 
panels change their position between logins
https://bugs.launchpad.net/bugs/15442
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