I ran into the same problem. Everything was working fine for me, until I
tried to change the screen resolution using the little System ->
Preferences -> Screen Resolution tool.

It seems that the gnome screen resolution setting interferes with the screen 
resolutions defined in xorg.conf for the two screens. To fix it, you can delete 
the gnome resolution setting from the configuration:
- run gconf-editor (from a terminal)
- navigate to desktop -> gnome -> screen -> default
- delete the 'rate' and 'resolution' entries (right click on them and choose 
'Unset')

Everything should be back to normal now.

-- 
xinerama broken on upgrade dapper to edgy beta
https://bugs.launchpad.net/bugs/63050
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