Martin-
Very similar setup on my end, except with a pair of nvidia GT9800's - circa 2008!. Also an onboard Intel HD4000 (disabled in bios). xrandr only showed 1 gpu, though all other sys related tools properly reported both. ubuntu 14.04 lts beta 2, nvidia 331.28 proprietary

The holy grail fix for me last night was: Base Mosaic! Empty xorg.conf, nvidia x server settings-> Enable Base Mosaic, then enable each detected display. It all just works! fast seemless multi-gpu, multi-head multi-monitor setup with 1 xscreen! My 3 displays are different resolutions and one is rotated portrait. Even the ubuntu Settings - Displays correctly shows all 3 monitors.

I suggest upgrading to the nvidia 331.28 proprietary drivers, blow out your xorg.conf, and try base Mosaic again.

-chad

➜ ~ nvidia-xconfig --query-gpu-info

 Number of GPUs: 2
 GPU #0:
 Name : GeForce 9800 GT
 UUID : GPU-56281125-01c7-ee85-b8b9-b3e5cf94b7c5
 PCI BusID : PCI:1:0:0
 Number of Display Devices: 1
 Display Device 0 (CRT-0):
 EDID Name : Samsung SyncMaster
 Minimum HorizSync : 30.000 kHz
 Maximum HorizSync : 81.000 kHz
 Minimum VertRefresh : 56 Hz
 Maximum VertRefresh : 75 Hz
 Maximum PixelClock : 146.250 MHz
 Maximum Width : 1680 pixels
 Maximum Height : 1050 pixels
 Preferred Width : 1680 pixels
 Preferred Height : 1050 pixels
 Preferred VertRefresh : 60 Hz
 Physical Width : 470 mm
 Physical Height : 300 mm
 GPU #1:
 Name : GeForce 9800 GT
 UUID : GPU-cbc59e3f-e8c1-a347-a069-b62f6b885f7d
 PCI BusID : PCI:2:0:0
 Number of Display Devices: 2
 Display Device 0 (CRT-0):
 EDID Name : Samsung SyncMaster
 Minimum HorizSync : 30.000 kHz
 Maximum HorizSync : 81.000 kHz
 Minimum VertRefresh : 56 Hz
 Maximum VertRefresh : 75 Hz
 Maximum PixelClock : 140.000 MHz
 Maximum Width : 1280 pixels
 Maximum Height : 1024 pixels
 Preferred Width : 1440 pixels
 Preferred Height : 900 pixels
 Preferred VertRefresh : 60 Hz
 Physical Width : 410 mm
 Physical Height : 270 mm

 Display Device 1 (DFP-1):
 EDID Name : Ancor Communications Inc ASUS VH242H
 Minimum HorizSync : 30.000 kHz
 Maximum HorizSync : 85.000 kHz
 Minimum VertRefresh : 55 Hz
 Maximum VertRefresh : 75 Hz
 Maximum PixelClock : 160.000 MHz
 Maximum Width : 1920 pixels
 Maximum Height : 1080 pixels
 Preferred Width : 1920 pixels
 Preferred Height : 1080 pixels
 Preferred VertRefresh : 60 Hz
 Physical Width : 520 mm
 Physical Height : 290 mm


Below is my xorg.conf - All of which x server settings generated. Note that it is quite straight forward, and does not even reference my second GPU.

 # nvidia-settings: X configuration file generated by nvidia-settings
 # nvidia-settings: version 331.20 (buildd@roseapple) Mon Feb 3 15:07:22 UTC 2014

 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 "Samsung SyncMaster"
 HorizSync 30.0 - 81.0
 VertRefresh 56.0 - 75.0
 Option "DPMS"
 EndSection

 Section "Device"
 Identifier "Device0"
 Driver "nvidia"
 VendorName "NVIDIA Corporation"
 BoardName "GeForce 9800 GT"
 BusID "PCI:1:0:0"
 EndSection

 Section "Screen"

 auto-select +3600+0 {rotation=right}, GPU-cbc59e3f-e8c1-a347-a069-b62f6b885f7d.GPU-1.DVI-I-3: nvidia-auto-select +1680+180"
 Identifier "Screen0"
 Device "Device0"
 Monitor "Monitor0"
 DefaultDepth 24
 Option "Stereo" "0"
 Option "nvidiaXineramaInfoOrder" "CRT-0"
 Option "metamodes" "GPU-56281125-01c7-ee85-b8b9-b3e5cf94b7c5.GPU-0.DVI-I-0: nvidia-auto-select +0+180, GPU-cbc59e3f-e8c1-a347-a069-b62f6b885f7d.GPU-1.DVI-I-0: nvidia-auto-select +3600+0 {rotation=right}, GPU-cbc59e3f-e8c1-a347-a069-b62f6b885f7d.GPU-1.DVI-I-3: nvidia-auto-select +1680+180"
 Option "MultiGPU" "Off"
 Option "SLI" "off"
 Option "BaseMosaic" "on"
 SubSection "Display"
 Depth 24
 EndSubSection
 EndSection