For those interested I figured it out.
I added this to my functions.php:
function set_the_terms_in_order ( $terms, $id, $taxonomy ) {
$terms = wp_cache_get( $id, "{$taxonomy}_relationships_sorted" );
if ( false === $terms ) {
$terms = wp_get_object_terms( $id, $taxonomy, array( 'orderby' => 'term_order' ) );
wp_cache_add($id, $terms, $taxonomy . '_relationships_sorted');
}
return $terms;
}
add_filter( 'get_the_terms', 'set_the_terms_in_order' , 10, 4 );
function do_the_terms_in_order () {
global $wp_taxonomies; //fixed missing semicolon
// the following relates to tags, but you can add more lines like this for any taxonomy
$wp_taxonomies['post_tag']->sort = true;
$wp_taxonomies['post_tag']->args = array( 'orderby' => 'term_order' );
}
add_action( 'init', 'do_the_terms_in_order');
then when I register my taxonomy I set:
'hierarchical' => false,
'orderby' => 'term_order'
CREDIT: http://wordpress.kdari.net/2011/07/listing-tags-in-custom-order.html