I think this is a major issue with the new wp_nav_menu function, I had the same problem, the way I have resolved it temporarily is to edit the wp-includes/nav-menu-template.php
Obviously this is only a temporary fix as editing the core files is never a good idea, as it will be overwritten everytime you upgrade. I’m hoping it will be fixed in the next version and that it will go back to class names instead of iD’s.
On line 79 of nav-menu-template.php, replace:
$output .= $indent . '<li id="menu-item-'. $item->ID . '"' . $value . $class_names .'>';
with:
$output .= $indent . '<li' . $value . $class_names .'>';
This will remove the ID from the li item.
On line 314, after:
foreach ( (array) $menu_items as $key => $menu_item ) {
$classes = (array) $menu_item->classes;
$classes[] = 'menu-item';
$classes[] = 'menu-item-type-' . $menu_item->type;
add:
$classes[] = 'menu-item-'. $menu_item->ID;
This will add the page-id as a li class (eg: page-item-6), as it used to in previous version of wordpress.
Hope this helps!
