Our shipping manager realized today that when he creates orders from the admin menu that attributes don't work. Basically it comes down to this code in the uc_order.js:

Line 274:

  $('#uc-order-add-product-form :input').each(
    function() {
      if ($(this).attr('name').substr(0, 10) == 'attributes') {
        post_vars[$(this).attr('name')] = $(this).val();
      }
    }
  );

I ran a debug on this, basically the array is being iterated through, resetting the post_vars attributes value to be the last one to iterate through. A simple addition to make sure the attribute is 'checked' will fix this bug:

  $('#uc-order-add-product-form :input').each(
    function() {
      if ($(this).attr('name').substr(0, 10) == 'attributes' && $(this).attr('checked')) {
        post_vars[$(this).attr('name')] = $(this).val();
      }
    }
  );