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[inode77 <1376832@xxxxxxxxxxxxxxxxxx>]

Happens to me too on HP Zbook 15 with (Nvidia/Intel) only Nvidia active.
Disabled intel card in bios.

Workaround:
Add "nogpumanager" to GRUB_CMDLINE_LINUX_DEFAULT in /etc/default/grub and execute update-grub to disable gpu-manger.

/var/log/gpu-manager.log 
log_file: /var/log/gpu-manager.log
last_boot_file: /var/lib/ubuntu-drivers-common/last_gfx_boot
new_boot_file: /var/lib/ubuntu-drivers-common/last_gfx_boot
grep dmesg status 256
dmesg status 256 == 0? No
Is nvidia loaded? yes
Was nvidia unloaded? no
Is nvidia blacklisted? no
Is fglrx loaded? no
Was fglrx unloaded? no
Is fglrx blacklisted? no
Is intel loaded? no
Is radeon loaded? no
Is radeon blacklisted? no
Is nouveau loaded? no
Is nouveau blacklisted? yes
Is fglrx kernel module available? no
Is nvidia kernel module available? yes
Vendor/Device Id: 10de:11fc
BusID "PCI:1@0:0:0"
Is boot vga? yes
Skipping "/dev/dri/card0", driven by "nvidia-drm"
Skipping "/dev/dri/card0", driven by "nvidia-drm"
Skipping "/dev/dri/card0", driven by "nvidia-drm"
Does it require offloading? no
last cards number = 2
Has amd? no
Has intel? no
Has nvidia? yes
How many cards? 1
The number of cards has changed!
Has the system changed? Yes
main_arch_path x86_64-linux-gnu, other_arch_path i386-linux-gnu
Current alternative: /usr/lib/nvidia-346/ld.so.conf
Current core alternative: (null)
Is nvidia enabled? yes
Is fglrx enabled? no
Is mesa enabled? no
Is pxpress enabled? no
Is prime enabled? no
Is nvidia available? yes
Is fglrx available? no
Is fglrx-core available? no
Is mesa available? yes
Is pxpress available? no
Is prime available? yes
System configuration has changed
Single card detected
Driver is already loaded and enabled
Nothing to do
System configuration has changed
Removing xorg.conf. Path: /etc/X11/xorg.conf

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Packages, which is subscribed to ubuntu-drivers-common in Ubuntu.
https://bugs.launchpad.net/bugs/1376832

Title:
  gpu-manager still deletes xorg.conf

Status in ubuntu-drivers-common package in Ubuntu:
  Confirmed

Bug description:
  
  To reproduce:

  1. Create /etc/X11/xorg.conf
  2. Wait until there is an update for some package (I don't know which one, suspect an nvidia driver one).
  3. Reboot.

  Result: gpu-manager deletes xorg.conf.

  Expected result: gpu-manager does not delete xorg.conf.

  Despite claims of a fix, this is still happening.

  ProblemType: Bug
  DistroRelease: Ubuntu 14.04
  Package: ubuntu-drivers-common 1:0.2.91.7
  ProcVersionSignature: Ubuntu 3.13.0-36.63-generic 3.13.11.6
  Uname: Linux 3.13.0-36-generic x86_64
  NonfreeKernelModules: nvidia
  ApportVersion: 2.14.1-0ubuntu3.4
  Architecture: amd64
  CurrentDesktop: XFCE
  Date: Thu Oct  2 17:36:03 2014
  InstallationDate: Installed on 2014-06-29 (94 days ago)
  InstallationMedia: Xubuntu 14.04 LTS "Trusty Tahr" - Release amd64 (20140416.2)
  SourcePackage: ubuntu-drivers-common
  UpgradeStatus: No upgrade log present (probably fresh install)

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