Ok, so here is the workaround... while we expect for a solution.

Considering my xorg file above, I added in "programs at session
startup", the following command:

xrandr --output default --mode 1280x1024

This uses the Modeline as defined in the xorg.conf file, and thus now
the xorg log shows:

...

[  3836.645] (II) No input driver specified, ignoring this device.
[  3836.645] (II) This device may have been added with another device file.

[  3836.994] (II) NVIDIA(0): Setting mode "1280x1024_60"
[  3842.916] (II) NVIDIA(0): Setting mode "1280x1024_85+0+0"

[  3844.405] (II) XKB: reuse xkmfile /var/lib/xkb/server-
A49B0D9CDBFA4DEADEE9D72BD5A2170E273505F0.xkm


As you can see, still the faulty setting to 60hz followed by the setting to 
85hz due to the session startup program xrandr

-- 
You received this bug notification because you are a member of Ubuntu-X,
which is subscribed to nvidia-settings in Ubuntu.
https://bugs.launchpad.net/bugs/949071

Title:
  CRT monitor refresh setting always resets to 60 after reboot

To manage notifications about this bug go to:
https://bugs.launchpad.net/ubuntu/+source/nvidia-settings/+bug/949071/+subscriptions

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