As of now get_post_meta returns value pairs in random order when used with multiple custom fields with the same key. It would be useful to either get the meta_id back for manual sorting or (better) having the result set returned ordered by meta_id which is the order they were entered.
Ran into trouble when I tried to match up several "pairs" of custom fields with same keys and fixed it by changing line 294 of /wp-includes/meta.php to:
$meta_list = $wpdb->get_results( $wpdb->prepare("SELECT $column, meta_key, meta_value FROM $table WHERE $column IN ($id_list) order by meta_id", $meta_type), ARRAY_A );
Simply added the "order by meta_id"..