jamesguy9

I found the solution!

I used the code from here: http://core.trac.wordpress.org/ticket/22070

I made the first fix the poster recommended and then I added the following code to line 468 of nav-menus.php:

<script type="text/javascript">
jQuery(function($) {
  // the currently displayed menu form
  var $form = $('#update-nav-menu');

  // Listen to new menus, since we have no possibility to hook
  // we have to interval it, because we can't capture an event here
  $('.submit-add-to-menu').click(function() {
    var $item_count = $form.find('.menu-item-handle').length;
    var $interval_id = setInterval(function() {
      var $current_item_count = $form.find('.menu-item-handle').length;
      if ($item_count < $current_item_count) {
        clearInterval($interval_id);
        // Add the dirty flag and set it to dirty immediately
        add_dirty_flags(1);
        // Reassign the mousedown/up events
        assign_mouse_events();
      }
    },200);
  });

  // add a hidden field, telling if the menu is dirty (by default, it's not)
  function add_dirty_flags($flag) {
    $form.find('.menu-item-handle').each(function() {
      if ($(this).find('.dirty-handle').length == 0) {
        var $html = '<input type="hidden" class="dirty-handle" value="' + $flag + '" />';
        $(this).append($html);
        console.log('flag added');
      }
    });
  }

  // (re)assigns mouse events to menu items
  function assign_mouse_events() {
    var $menu_items = $('.menu-item-bar');
    // Unbind previously assigned events
    $menu_items.unbind('mouseup').unbind('mousedown');

    // Dirty Flag handler if a click happens
    $menu_items.mousedown(function() {
      $(this).find('.dirty-handle').val('1');
    });

    // if the parent changes on release the mouse handle, change all items with the new parent to dirty
    $menu_items.mouseup(function() {
      menu_save_mouseup($(this));
    });
  }

  // The call back for mouseup on menu bars
  function menu_save_mouseup($this) {
    var $temp_object = $this.parent();
    // Mark everything with the same parent dirty
    setTimeout(function() {
      var $parent_id = $temp_object.find('.menu-item-data-parent-id').val();
      // Go through all fields, dirtying everything that has the same parent
      $('.menu-item-data-parent-id').each(function() {
        if ($(this).val() == $parent_id)
          $(this).parent().prev().find('.dirty-handle').val('1');
      });
    },200);
  }

  // On submit make every undirty menu an empty title, so it won't get saved
  // We're using a hoax in nav-menus.php, line 335 here..
  $form.submit(function() {
    // Now traverse all handles and make only dirties saveable
    $form.find('.menu-item-handle').each(function() {
      // Find the dirty flag
      var $is_dirty = $(this).find('.dirty-handle').val();
      $(this).find('.dirty-handle').remove();
      if ($is_dirty == 0) {
        // The div containing the menu informations
        var $forms = $(this).parent().next();
        // Remove the title value so it doesn't get saved
        $forms.find('.edit-menu-item-title').val('');
      }
    });
    return true;
  });

  // Assign mouse events on first load
  assign_mouse_events();
  // Add all dirty flags (not dirty by default of course)
  add_dirty_flags(0);
});
</script>

This makes the menu actually save and do so quickly.

It’s a very large site which, unfortunately, requires many nav items.

Thanks again for your help.