What works for me:
function jsUpdateCart()
..
url: "<?php echo site_url() . 'shop/ajax_cart';?>",
..
EDIT: i put the
JS code in the template.php ..
EDIT2 : i use JQuery but with scriptaculous may seem like this, if you put the script in template.php file:
var ajax = new Ajax.Updater(
'ajax_msg', <?php echo site_url() . 'welcome/ajax_cart';?>, {method:'post',parameters:params,onComplete:showMe ssage}
);
trust me, 100% working this way