Querying custom taxonomy on category-specific page is overwritten by function

Not 100% sure if this will work, but have you tried querying the meta key in a seperate array inside the $args? For instance…

$args = array(
    'category' => 2042,
    'posts_per_page' => 3,
    'orderby' => 'meta_value',
    'meta_query' => array (
        array (
          'key' => 'vacation_order',
          'compare' => 'IN'
        )
    ) );        

$new_query = new WP_Query( $args );
$myposts = get_posts( $args );
foreach( $myposts as $post ) :  setup_postdata($post);

Was just a thought, as I said, not tested.