@mitu Thanks for the help - you're right I did have a settings override for the core, and I had no idea those settings contained the screen mode as well.
So I had to delete the settings override file for the core, then set my screenmode in runcommand, then save my settings override again. All working now.
Please do not post a support request without first reading and following the advice in https://retropie.org.uk/forum/topic/3/read-this-first