Unability to change monitor resolutions&position (Thinkpad P50, Nvidia Quadro M1000M, with docking station)

I have 2 monitors connected into P50’s docking station (one VGA, one DVI). My desired layout is: notebook monitor (DP-4) on the left, right of it first monitor(DP-3.2) (rotated 90degrees), right of it second monitor (DP-3.3). Every monitor has 1920x1080 resolution.
But somehow I’m stuck with different layout (from left: rotated DP-3.2, DP-3.3, DP-4).
When I run nvidia-settings and change layout there and confirm, the monitors flicker for a while (it looks like it is trying the layout I want), but after few seconds I’m back at the wrong layout.
This is snippet of output of /var/log/Xorg.0.log when I confirm the new layout:

[ 562.601] (II) NVIDIA(0): Setting mode "DPY-6:nvidia-auto-select+0+0,DPY-0:nvidia-auto-select+1920+0{rotation=right
[ 564.179] (II) NVIDIA(0): Setting mode "DP-4: nvidia-auto-select @1920x1080 +0+0 {ViewPortIn=1920x1080, ViewPortOut=1920x1080+0+0, Rotation=270}, DP-3.3: nvidia-auto-select @1920x1080 +3000+0 {ViewPortIn=1920x1080, ViewPortOut=1920x1
[ 565.665] (II) NVIDIA(0): Setting mode "DP-4: nvidia-auto-select @1920x1080 +0+0 {ViewPortIn=1920x1080, ViewPortOut=1920x1080+0+0, Rotation=270}, DP-3.3: nvidia-auto-select @1920x1080 +1080+0 {ViewPortIn=1920x1080, ViewPortOut=1920x1
[ 567.043] (II) NVIDIA(0): Setting mode "DP-4: nvidia-auto-select @1920x1080 +3000+0 {ViewPortIn=1920x1080, ViewPortOut=1920x1080+0+0, Rotation=270}, DP-3.3: nvidia-auto-select @1920x1080 +1080+0 {ViewPortIn=1920x1080, ViewPortOut=192

I really don’t grok what is the DPY-6, when my monitors are DP-4, DP-3.2 and DP-3.3.
I tried to delete /etc/X11/xorg.conf and generate new, deleting ~/.nvidia-settings-rc and ~/.nv.

I’m on Fedora 26. I’ve tried nvidia drivers installed from rpmfusion and from https://negativo17.org/nvidia-driver/

In this google drive are two tarballs generated by nvidia-bug-report.sh: https://drive.google.com/drive/folders/0B9OUl4QZrhPFak95UC1jQ0tJVEE?usp=sharing

Even turning the two external monitors in nvidia-settings does nothing. Nvidia-settings says they are turned off, but in fact they aren’t (still stuck with wrong layout). Pushing “Detect Displays” or restarting nvidia-config shows the wrong layout again.

Doesn’t the gnome monitor manager work? Alternatively, use the appropriate xrandr commands?

I’m using Plasma and its monitor management does the same thing as nvidia-settings. Doing ‘xrandr --output DP-4 --auto --output DP-3.2 --right-of DP-4 --auto --output DP-3.3 --right-of DP-3.2 --auto’ which imho should do what I want does the same as nvidia-setting and plasma monitor management software. The monitors blinks (trying to apply new settings) and then falls back to the wrong dayout.

Well read this, dpy-6 is just some name aliase for one of your display outputs:
https://us.download.nvidia.com/XFree86/Linux-x86/375.39/README/displaydevicenames.html

Does creating a xorg ServerLayout section with the desired layout work?
ftp://www.x.org/pub/xorg/X11R6.8.1/doc/DESIGN2.html