More info. So normally I had the minimal xorg configuration, and would
just use twinview when plugging in an external monitor.

I switched it to this:


# nvidia-settings: X configuration file generated by nvidia-settings
# nvidia-settings:  version 280.13  (buildd@yellow)  Fri Aug  5 12:31:28 UTC 
2011

Section "ServerLayout"
    Identifier     "Layout0"
    Screen      0  "Screen0" 0 0
    InputDevice    "Keyboard0" "CoreKeyboard"
    InputDevice    "Mouse0" "CorePointer"
    Option         "Xinerama" "0"
EndSection

Section "Files"
EndSection

Section "InputDevice"
    # generated from default
    Identifier     "Mouse0"
    Driver         "mouse"
    Option         "Protocol" "auto"
    Option         "Device" "/dev/psaux"
    Option         "Emulate3Buttons" "no"
    Option         "ZAxisMapping" "4 5"
EndSection

Section "InputDevice"
    # generated from default
    Identifier     "Keyboard0"
    Driver         "kbd"
EndSection

Section "Monitor"
    # HorizSync source: edid, VertRefresh source: edid
    Identifier     "Monitor0"
    VendorName     "Unknown"
    ModelName      "Apple"
    HorizSync       30.0 - 75.0
    VertRefresh     60.0
    Option         "DPMS"
EndSection

Section "Device"
    Identifier     "Device0"
    Driver         "nvidia"
    VendorName     "NVIDIA Corporation"
    BoardName      "GeForce 9600M GT"
EndSection

Section "Screen"
    Identifier     "Screen0"
    Device         "Device0"
    Monitor        "Monitor0"
    DefaultDepth    24
    Option         "TwinView" "1"
    Option         "metamodes" "DFP-0: nvidia-auto-select +0+0, DFP-1: 
nvidia-auto-select +1440+0"
    SubSection     "Display"
        Depth       24
    EndSubSection
EndSection


And on first boot/login, the monitor works fine. However, If I open up 
nvidia-settings and disable the external monitor, nvidia settings complains but 
no more windows are placed on it (the mouse can still traverse into it).

Upon re-adding the external monitor to TwinView, however, this effect
happens again.. black area where mouse can traverse but no windows.
Logging out / back in "fixes" this, but that means loss of my session.

So it seems that whatever method nvidia settings uses to re-configure
displays isn't being honored by Unity.

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https://bugs.launchpad.net/bugs/813343

Title:
  nvidia drivers, second monitor covered by black

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