So are you saying that changing the code in utility-functions.php at line number 450 to –
$query_args = array('post_type' => 'portfolio', 'posts_per_page' => $args['posts_per_page'], 'filterable' => $args['filterable'], 'paged' => $paged);
did not fix the issue? I could try it here but I cannot reproduce the ordering issue somehow on any of my installations when the above code is in place (all themes of mine except Extinct have the above code and hence I can revert back to the old one for Extinct too if custom order is no big benefit for most). And again, have not had anyone report it so far honestly.