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I am currently using Ubuntu 15.04 with a GTX 570 on 346.46. I have a 2560x1440 display with a 1080x1920 (portrait) display to the right. I am using i3 as a window manager. The displays seem to be set up correctly in Unity with Ubuntu's display settings; this issue does occur in gnome, i3, and the login screen (Ubuntu default). I have used nvidia-settings to modify the layout and generate an xorg.conf, which is indeed located in /etc/X11/xorg.conf. Its contents are the following

# nvidia-settings: X configuration file generated by nvidia-settings
# nvidia-settings:  version 346.59  (buildd@tipua)  Wed Apr 15 14:33:47 UTC 2015

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      "Ancor Communications Inc ASUS PB278"
    HorizSync       24.0 - 99.0
    VertRefresh     50.0 - 75.0
    Option         "DPMS"
EndSection

Section "Device"
    Identifier     "Device0"
    Driver         "nvidia"
    VendorName     "NVIDIA Corporation"
    BoardName      "GeForce GTX 570"
EndSection

Section "Screen"
    Identifier     "Screen0"
    Device         "Device0"
    Monitor        "Monitor0"
    DefaultDepth    24
    Option         "Stereo" "0"
    Option         "nvidiaXineramaInfoOrder" "DFP-0"
    Option         "metamodes" "DVI-I-2: nvidia-auto-select +0+240, DVI-I-3: nvidia-auto-select +2560+0 {rotation=left}; DVI-I-2: nvidia-auto
-select +0+0; DVI-I-2: 1920x1080 +0+0; DVI-I-2: 1680x1050 +0+0; DVI-I-2: 1440x900 +0+0; DVI-I-2: 1280x1024 +0+0; DVI-I-2: 1280x1024_60 +0+0; 
DVI-I-2: 1280x960 +0+0; DVI-I-2: 1280x800 +0+0; DVI-I-2: 1280x720 +0+0; DVI-I-2: 1152x864 +0+0; DVI-I-2: 1024x768 +0+0; DVI-I-2: 1024x768_70 
+0+0; DVI-I-2: 1024x768_60 +0+0; DVI-I-2: 800x600 +0+0; DVI-I-2: 800x600_72 +0+0; DVI-I-2: 800x600_60 +0+0; DVI-I-2: 800x600_56 +0+0; DVI-I-2
: 640x480 +0+0; DVI-I-2: 640x480_60 +0+0; DVI-I-2: nvidia-auto-select +0+0 {viewportin=1920x1200, viewportout=2304x1440+128+0}; DVI-I-2: nvid
ia-auto-select +0+0 {viewportin=1600x1200, viewportout=1920x1440+320+0}; DVI-I-2: nvidia-auto-select +0+0 {viewportin=1366x768, viewportout=2
560x1439+0+0}"
    Option         "SLI" "Off"
    Option         "MultiGPU" "Off"
    Option         "BaseMosaic" "off"
    SubSection     "Display"
        Depth       24
    EndSubSection
EndSection

Although the file does seem to be written to the correct error, I get the following error when writing with nvidia-settings:

Package xorg-server was not found in the pkg-config search path.
Perhaps you should add the directory containing `xorg-server.pc'
to the PKG_CONFIG_PATH environment variable
No package 'xorg-server' found
Package xorg-server was not found in the pkg-config search path.
Perhaps you should add the directory containing `xorg-server.pc'
to the PKG_CONFIG_PATH environment variable
No package 'xorg-server' found

When I reboot my PC, the portrait display is once again in its default configuration (landscape). This is fixed by using nvidia-settings and setting everything to the same values, although I believe this should be fixed by the X11 config file.

I also get a system error of my nvidia driver not being a Ubuntu package, which seems to have started after upgrading from 14.04 to 15.04 via do-release-upgrade.

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