Use WP_Query To Alter The Posts Per Page Of A Custom Taxonomy Term Archive Of A Custom Post Type. When using Post Types Order plugin ( ) add: 'orderby' => 'menu_order', to the $args

gistfile1.php

<?php
//* Replace the standard loop with our custom loop
//* props to David Wang, he is the man!
// @author David Wang
// @link http://genesissnippets.com/genesis-custom-loop/

remove_action( 'genesis_loop', 'genesis_do_loop' );
add_action( 'genesis_loop', 'child_do_custom_loop' );
 
function child_do_custom_loop() {
 
    global $paged; // current paginated page
    global $query_args; // grab the current wp_query() args
    $args = array(
	'paged' 		 	=> $paged, // respect pagination
        'post_type'	  	 	=> 'portfolio',
        'taxonomy' 	  		=> 'portfolio_cat',
        'term'		    		=> 'media-analyst',
        'posts_per_page' 	=> '18',
        'orderby  '	  	 	=> 'menu_order', // for use with http://wordpress.org/plugins/post-types-order/
    );
 
    genesis_custom_loop( wp_parse_args($query_args, $args) );
 
}