My normal desktop session has a virtual fb of 2560x1024
(two 17" TFTs at 1024x768 each). When I log in, I normally
move my panel (I only use one) from the left display to the
right (Ideally it would just stick to the right, but that's
another matter :))

If, outside of this gnome session, I create a vncserver,
this starts with a gnome session inside it. Once that has
been created, my desktop panel moves back to the left
monitor.

I don't think the second gnome session should interfere
with the first.

I'm not 100% sure the session is at fault, maybe having two
metacity instances running is the culprit -- please excuse
my ignorance and reassign as appropriate.