I have just struggled with a similar issue for the last several days:
Ubuntu 9.04 (AMD64) with NVidia drivers
I have a primary monitor in 1024x768 and a projector in 1920x1080 and prefer to 
run with separate x-screens. This worked fine in Ubunty 8.04, but with Ubuntu 
9.04 the 2nd screen did not work properly.

After a bunch of messing around I finally realized that the problem is that 
there is no "screen1" directory in /.gconf/apps/compiz. There is a "screen0" 
directory there though. To fix the issue I did the following:
1) Installed CompizConfig Manager using "- sudo apt-get install 
compizconfig-settings-manager"
2) In the CompizConfig Settings Manager -> General Options -> Display Settings
        - Disabled "Detect Outputs"
        - Set Outputs to "1024x768+0+0"
3) In a terminal
        - cd .gconf/apps/compiz
        - mkdir screen1
        - cp -r screen0/* screen1
        - cd screen1/options
        - vi %gconf.xml  --> Modified resolution to "1920x1080" 
4) I rebooted and everything works fine (except the mouse still has that odd 
behavior)

-- 
Separate X screen blank in Jaunty (nvidia)
https://bugs.launchpad.net/bugs/366743
You received this bug notification because you are a member of Ubuntu-X,
which is subscribed to nvidia-graphics-drivers-180 in ubuntu.

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