I found the trouble with this. It has to do with the scporder_next_post_where and the scporder_previous_post_where.
In deed, in this function, you overwrite the WHERE condition for the sql so that the $in_same_term variable doesn’t work anymore.
A quick fix would be to replace in the scporder_next_post_where function :
$where = "WHERE p.menu_order > '" . $current_menu_order . "' AND p.post_type = '" . $post->post_type . "' AND p.post_status = 'publish'";
with that :
$where .= " AND p.menu_order < '" . $current_menu_order . "' AND p.post_type = '" . $post->post_type . "' AND p.post_status = 'publish'";
and for the scporder_previous_post_where function :
$where = "WHERE p.menu_order > '" . $current_menu_order . "' AND p.post_type = '" . $post->post_type . "' AND p.post_status = 'publish'";
with this :
$where .= " AND p.menu_order > '" . $current_menu_order . "' AND p.post_type = '" . $post->post_type . "' AND p.post_status = 'publish'";
Please fix this ASAP.