I can confirm this is also a problem with three displays. When I run "gnome-settings-daemon --replace" it does restore the proper order, but the main display is still set to the wrong one, and there is a virtual desktop larger than the actual screen resolution on one of the monitors. (I can put the mouse to the far right corner and all displays shift to the left, revealing a gray bar outside of the wallpaper.) I believe this is because I have settings in xorg.conf to compensate for the overscan on one of the monitors, but perhaps Pantheon doesn't recognize that.
I can correct this by opening NVIDIA X Server Settings, making some minor change to X Server Display Configuration to enable the "Apply" button, and clicking apply. I need to do this on each logon.
I can confirm this is also a problem with three displays. When I run "gnome- settings- daemon --replace" it does restore the proper order, but the main display is still set to the wrong one, and there is a virtual desktop larger than the actual screen resolution on one of the monitors. (I can put the mouse to the far right corner and all displays shift to the left, revealing a gray bar outside of the wallpaper.) I believe this is because I have settings in xorg.conf to compensate for the overscan on one of the monitors, but perhaps Pantheon doesn't recognize that.
I can correct this by opening NVIDIA X Server Settings, making some minor change to X Server Display Configuration to enable the "Apply" button, and clicking apply. I need to do this on each logon.