Thanks for the wp_usermeta hint Elliot – that solved it for me.
Just been tackling this problem for an hour (thinking it was me being stupid), then found this thread, and checked the wp_usermeta table. I deleted a couple of rows with my user id and the meta_keys:
meta-box-order_{custom_post_id}
metaboxhidden_{custom_post_id}
and now my field groups are displaying in the correct order, as defined by the Order No. meta field.
