Multiple loop for “featured” items returns wrong posts

Your second loop is fine because it works – although it is probably more efficient to do it this way:

$args = array( 'post_type' => 'onourradar', 'posts_per_page' => -1, 'orderby' => 'menu_order', 'order' => 'ASC', 'offset' => '2');
$my_query = new WP_Query($args);
while ($my_query->have_posts()) : $my_query->the_post();

The difference is that a do_not_duplicate query is just not a very efficient way to do things (although sometimes it is necessary). Using the offset is definitely a better way to go.