AJAX commands and Drupal Messages

Hi, we are having a little bit of trouble adding ajax to the COMMERCE MODULE Add to Cart form so it changes some elements besides the Shopping Cart.

This is our code in the hook_form_FORM_ID_alter() function to add Ajax support:

$form['#submit'][] = 'MYMODULE_add_to_cart_form_submit';
$form['submit']['#ajax'] = array(
  'callback' => 'MYMODULE_add_to_cart_form_ajax',
  'wrapper' => 'shoppingcart', // Our Shopping Cart VIEW has an id="shoppingcart".
  'method' => 'replace',
  'effect' => 'none',
  'progress' => array('type' => 'none'), // Don't want any throbber or progress bar.
);

In our submit function the only thing we are doing here is to REBUILD our form. We got this from reading this help http://api.drupal.org/api/drupal/includes--form.inc/function/drupal_rebu...

function MYMODULE_add_to_cart_form_submit($form, &$form_state) {
  // This rebuilds the form from cache and invokes the defined #ajax['callback'].
  $form_state['rebuild'] = TRUE;
}

So our main problem here is about about Drupal Messages.

If we use this code on our AJAX callback function...

function MYMODULE_add_to_cart_form_ajax($form, $form_state) {
  $uid = $form['uid']['#value'];
  $cart_order = commerce_cart_order_load($uid);
  $shoppingcart = commerce_embed_view('commerce_cart_block', 'default', array($cart_order->order_id));
  return $shoppingcart;
}

...then the Shopping Cart View is updated correctly AND a Drupal Message is added to the Shopping Cart Block, which is not a problem because we can move it to the correct location (via jQuery).

But we want to change more elements apart from the Shopping cart so we tried using Ajax COMMANDS in our AJAX callback function. We re-wrote our function to...

function MYMODULE_add_to_cart_form_ajax($form, $form_state) {
  $uid = $form['uid']['#value'];
  $cart_order = commerce_cart_order_load($uid);
  $shoppingcart = commerce_embed_view('commerce_cart_block', 'default', array($cart_order->order_id));

  $commands = array();
  $commands[] = ajax_command_replace('#full-node-shoppingcart', $shoppingcart);
  // We add here more commands but for the purpose of this example we add only one.

  return array('#type' => 'ajax', '#commands' => $commands);
}

...here the Shopping Cart View is updated correctly BUT no message is sent. In the next page full load (F5) it shows as a normal Drupal message. So if a user adds a Product and then goes to his Profile, the "Product has been added to your cart" message is shown in the Profile page. This also applies to validation errors (no stock for that quantity).

Is there a way to use ajax commands and still get the first functionality (the message is sent by Ajax so is not shown in the next page load)?
Thanx in advance.