I no longer see the problem on Ubuntu 13.10. Both monitors show as DVI
connected and both work fine.

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https://bugs.launchpad.net/bugs/890061

Title:
  Nouveau thinks secondary DVI connection is HDMI - monitor blank

Status in “xserver-xorg-video-nouveau” package in Ubuntu:
  Incomplete

Bug description:
  Fresh install of 11.10 amd64 on a machine with a dual head nVidia card
  (shown by lspci as "nVidia Corporation G92 [GeForce GTS 250] rev a2")
  with twin DVI outputs and a primary 30" monitor and secondary 23"
  monitor, both connected via DVI. After 11.10 install completed, the
  right-hand 23" monitor remains blank and in power save, although when
  I open System Settings / Displays, both monitors appear there with the
  initial display configuration showing as mirrored displays at 1152x864
  resolution. Un-mirroring the displays and setting each display to its
  native resolution and orientation still has the LH monitor blank. I
  think the problem is that the 23" monitor is being incorrectly
  detected as being connected via HDMI, as when I run xrandr in a
  terminal it shows

  ===================================================
  nick@ubuntu1110:~$ xrandr
  Screen 0: minimum 320 x 200, current 3640 x 1920, maximum 8192 x 8192
  DVI-I-1 connected 2560x1600+0+0 (normal left inverted right x axis y axis) 
641mm x 401mm
     2560x1600      60.0*+
     1920x1440      60.0  
     1920x1200      59.9  
     1600x1200      60.0  
     1280x1024      75.0     60.0  
     1280x800       59.8  
     1152x864       75.0  
     1024x768       75.1     60.0  
     800x600        75.0     60.3  
     640x480        75.0     60.0  
     720x400        70.1  
  HDMI-1 connected 1080x1920+2560+0 right (normal left inverted right x axis y 
axis) 509mm x 286mm
     1920x1080      60.0*+
     1280x1024      75.0     60.0  
     1152x864       75.0  
     1024x768       75.1     60.0  
     800x600        75.0     60.3  
     640x480        75.0     60.0  
     720x400        70.1
  ===================================================

  The video card does not have any HDMI output at all, just the two DVI
  outputs.

  ProblemType: Bug
  DistroRelease: Ubuntu 11.10
  Package: xserver-xorg-video-nouveau 1:0.0.16+git20110411+8378443-1
  ProcVersionSignature: Ubuntu 3.0.0-12.20-generic 3.0.4
  Uname: Linux 3.0.0-12-generic x86_64
  .tmp.unity.support.test.0:
   
  ApportVersion: 1.23-0ubuntu4
  Architecture: amd64
  CompizPlugins: 
[core,bailer,detection,composite,opengl,decor,grid,vpswitch,mousepoll,move,wall,place,gnomecompat,imgpng,regex,snap,compiztoolbox,resize,session,animation,expo,workarounds,ezoom,staticswitcher,fade,scale]
  CompositorRunning: None
  Date: Mon Nov 14 14:32:07 2011
  DistUpgraded: Fresh install
  DistroCodename: oneiric
  DistroVariant: ubuntu
  ExtraDebuggingInterest: Yes, whatever it takes to get this fixed in Ubuntu
  GraphicsCard:
   nVidia Corporation G92 [GeForce GTS 250] [10de:0615] (rev a2) (prog-if 00 
[VGA controller])
     Subsystem: nVidia Corporation Device [10de:0592]
  InstallationMedia: Ubuntu 11.10 "Oneiric Ocelot" - Release amd64 (20111011)
  MachineType: System manufacturer System Product Name
  ProcEnviron:
   LANGUAGE=en_AU:en
   PATH=(custom, no user)
   LANG=en_AU.UTF-8
   SHELL=/bin/bash
  ProcKernelCmdLine: BOOT_IMAGE=/boot/vmlinuz-3.0.0-12-generic 
root=UUID=94d1d51f-68be-488e-b037-37e7b871a7a7 ro quiet splash vt.handoff=7
  SourcePackage: xserver-xorg-video-nouveau
  UpgradeStatus: No upgrade log present (probably fresh install)
  XorgConf:
   Section "Device"
   Identifier "n"
   Driver "nouveau"
   EndSection
  dmi.bios.date: 09/21/2010
  dmi.bios.vendor: American Megatrends Inc.
  dmi.bios.version: 1408
  dmi.board.asset.tag: To Be Filled By O.E.M.
  dmi.board.name: P6T
  dmi.board.vendor: ASUSTeK Computer INC.
  dmi.board.version: Rev 1.xx
  dmi.chassis.asset.tag: Asset-1234567890
  dmi.chassis.type: 3
  dmi.chassis.vendor: Chassis Manufacture
  dmi.chassis.version: Chassis Version
  dmi.modalias: 
dmi:bvnAmericanMegatrendsInc.:bvr1408:bd09/21/2010:svnSystemmanufacturer:pnSystemProductName:pvrSystemVersion:rvnASUSTeKComputerINC.:rnP6T:rvrRev1.xx:cvnChassisManufacture:ct3:cvrChassisVersion:
  dmi.product.name: System Product Name
  dmi.product.version: System Version
  dmi.sys.vendor: System manufacturer
  version.compiz: compiz 1:0.9.6+bzr20110929-0ubuntu5
  version.ia32-libs: ia32-libs N/A
  version.libdrm2: libdrm2 2.4.26-1ubuntu1
  version.libgl1-mesa-dri: libgl1-mesa-dri 7.11-0ubuntu3
  version.libgl1-mesa-dri-experimental: libgl1-mesa-dri-experimental N/A
  version.libgl1-mesa-glx: libgl1-mesa-glx 7.11-0ubuntu3
  version.xserver-xorg: xserver-xorg 1:7.6+7ubuntu7
  version.xserver-xorg-input-evdev: xserver-xorg-input-evdev 1:2.6.0-1ubuntu13
  version.xserver-xorg-video-ati: xserver-xorg-video-ati 
1:6.14.99~git20110811.g93fc084-0ubuntu1
  version.xserver-xorg-video-intel: xserver-xorg-video-intel 2:2.15.901-1ubuntu2
  version.xserver-xorg-video-nouveau: xserver-xorg-video-nouveau 
1:0.0.16+git20110411+8378443-1

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