What you are experiencing is the WP remembers where meta boxes are positioned and it is not a function of ACF. When any user moves a metabox WP remembers where is was moved to and displays in that location until they move it again. WP stores this information in the DB in the _usermeta table for each user. The meta_key of these entries is "meta-box-order_{$screen}". This will even override the position you set for a field group if you change it after the value is added to the DB. The only way to reset this is to do into the DB and delete these entries.
There is a plugin but it only works for the currently logged in user and I do not know if it works for CPTs or on Taxonoies. https://wordpress.org/plugins/reset-meta-box-positions/
