Problem
The 'bundle' property of menu links should be derived from the 'menu_name' property. On load this happens, but not when creating a new bundle. In that case, the class default of 'tools' is not overridden.
<?php
$menu_link = entity_create(array('menu_name'=> 'foo'));
print $menu_link->bundle; // This should be 'foo', but is actually 'tools'.
?>Related Issues
See also #1966298-91: Introduce menu link bundles per menus and #115-117