WordPress has a habit of remembering the order that meta boxes are displayed and showing them in that order the next time the page is loaded. This can override the values that you set for the display order you set in the order no value of the field group. WP saves the order that you last saw the field when a post is saved and this also happens during a WP autosave.
This value is stored in the database in the usermeta table with the meta_key of met-box-order_{$post_type}
Once this value is saved by WP the only way you can change the order of the meta boxes is to drag them to a different position while looking at the edit post page. You can also delete this value from the database and that will reset the display order of the meta boxes to their original configuration. This is so that each person can reorder the boxes to their own preferences. WP does not have a way to reset this without manually deleting the values from the DB.
Check out this post on Stack Exchange: http://wordpress.stackexchange.com/questions/38646/reset-positions-of-metaboxes-in-admin
