I've identified one problem source.
At least sometimes after a power off shut down it comes up with the
laptop display selected as primary.
How can I force it to always come up with the VGA monitor as primary?
I created /home/richard/.screenlayout/VGA-as-master.sh with preferred
settings back when I was experimenting. I had understood ARandR would
use it automatically. It evidently doesn't.
perhaps you need to create xorg.conf (at least this is what I did)
and set up there the outputs in the order you want them.
Another perhaps better option is to get udev or whatever assigns the
outputs of the graphic card to do it constantly.
The DE most likely takes what it gets. Some DEs can talk to xrandr
so you can store and restore the settings, but I don't know arandr.
regards