I have a similar problem, but it doesn't occur every time.

I have two screens - laptop at 1600x1024 and external at 1600x1200.
Often at startup, both of my panels which are on the laptop screen end
up on the external screen instead. Sometimes I restart X and they load
correctly.

I also noticed that, when this happens, the wallpaper ends up the size
of the laptop screen, rather than stretched across both screens, and the
right-click only has an effect on that region.

I'm guessing that sometimes, Gnome does not find both screens
immediately, so it sets the desktop size to the size of the only screen
it finds and places all panels on it, then by the time everything is
loaded both screens are available so that the panels end up on the
leftmost screen.

I have Ubuntu 8.10, Intel Mobile GM965/GL960 onboard graphics chip

Added the above info to the Gnome bug report

-- 
dual screen all panels end up on one screen at startup
https://bugs.launchpad.net/bugs/290935
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