@Alistair: the system didn't really change in your case. It's just that
when you first run gpu-manager, it will have no records on any previous
runs (comparing "last cards number = 0" with "How many cards? 1"), so it
will try to configure your system. It should only happen the first time,
unless you manually delete /var/lib/ubuntu-drivers-common/last_gfx_boot
, that is.

@David: passing the "nogpumanager" parameter on boot is enough. 18
seconds is a really long time, I'm not sure that is the problem. Seeing
your log might have helped.

@inode: disabling a GPU in the bios will make gpu-manager reconfigure
your xorg.conf for you (only the first time, until you re-enable the
GPU, etc.). If you don't like that behaviour, the boot parameter is ok
for you to use.

@Manuel: sorry but your log only shows that gpumanager is disabled, so
it's not much help to me. You didn't even describe how or when the
"problem" happened, so I'm not sure how to help.

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https://bugs.launchpad.net/bugs/1376832

Title:
  gpu-manager still deletes xorg.conf

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