I just installed Ubuntu 17.10 on my Asus n56vz laptop with two external displays connected and found that display settings (primary display, positions, etc.) are not saved (are not kept after reboot). Also, I faced with a problem editing display positions (drag and drop doesn't work well).
Possibly, it happens because of two configurations in
monitors.xml file. The first one is active when laptop lid is closed and has two external displays. The second one is active when laptop lid is opened and has three displays (internal and external ones).
Update, I tried to update 'monitors.xml' manually, it looks like that it is not used at all.
Update, I was able to fix it, and to enable my laptop to remember display settings by disabling laptop lid opening handling setting 'IgnoreLid=true' in '/etc/UPower/UPower.conf' file.
There are several similar questions on askubuntu, but no clear answers.