I have a similar problem:
I have been using until today ubuntu 10.4, I did not bother upgrading it since it worked and I need a working station in my office. It work under strange configuration: I used xinerama in the xorg.conf file (find it in /etc/X11/) and rotated the screens with the options given by the nvidia driver
Option "Rotate" "left"
It worked, I wrote it long time ago. Now, I wanted to try ubuntu 3D or Gnome 3D, but it dones not work, maybe because xinerama does not work with thi nvidia driver and the 12.04 release. It DOES work with ubuntu 12.04 if you choose 'gnome classic', but not otherwise.
I tried to tweek with nvidia-settings program, but did not find any option to rotate the screens there.
here is the xorg.conf:
Section "Screen"
Identifier "Main"
Device "nvidia A"
Monitor "Dell-VGA"
Option "RenderAccel" "true"
Option "AllowGLXWithComposite" "true"
Option "AddARGBGLXVisuals" "true"
Option "Rotate" "left"
DefaultDepth 24
SubSection "Display"
Depth 24
Modes "2160x1900@60" "2100x1600@60" "1536x1280@60" "1200x800@60" "1800x1440@60"
EndSubSection
EndSection
Section "Screen"
Identifier "Second"
Device "nvidia B"
Monitor "Dell-DVI"
DefaultDepth 24
Option "RenderAccel" "true"
Option "AllowGLXWithComposite" "true"
Option "AddARGBGLXVisuals" "true"
Option "Rotate" "left"
SubSection "Display"
Depth 24
Modes "2160x1900@60" "2100x1600@60" "1536x1280@60" "1200x800@60" "1800x1440@60"
EndSubSection
EndSection
Section "Module"
Load "dbe"
Load "extmod"
Load "type1"
Load "freetype"
Load "glx"
EndSection
# commented out by update-manager, HAL is now used
#Section "InputDevice"
# Identifier "Keyboard0"
# Driver "keyboard"
#EndSection
# commented out by update-manager, HAL is now used
#Section "InputDevice"
# Identifier "Mouse0"
# Driver "mouse"
# Option "Protocol" "auto"
# Option "Device" "/dev/psaux"
# Option "Emulate3Buttons" "no"
# Option "ZAxisMapping" "4 5"
#EndSection
Section "ServerLayout"
Identifier "Default Layout"
Screen 0 "Main" 0 0
Screen 1 "Second" RightOf "Main"
# commented out by update-manager, HAL is now used
# InputDevice "Keyboard0" "CoreKeyboard"
# commented out by update-manager, HAL is now used
# InputDevice "Mouse0" "CorePointer"
Option "Xinerama" "true"
EndSection
Section "Device"
Identifier "nvidia A"
BoardName "nv"
BusID "PCI:01:00:0"
Screen 0
Driver "nvidia"
Option "NoLogo" "True"
EndSection
Section "Device"
Identifier "nvidia B"
BoardName "nv"
BusID "PCI:01:00:0"
Screen 1
Driver "nvidia"
Option "NoLogo" "True"
EndSection
Again, I get dual screens, rotated properly with this conf file, but only on gnome classic login, not unity or 3D.