Index: includes/menu.inc
===================================================================
RCS file: /cvs/drupal/drupal/includes/menu.inc,v
retrieving revision 1.255.2.28
diff -u -p -r1.255.2.28 menu.inc
--- includes/menu.inc	9 Feb 2009 16:28:21 -0000	1.255.2.28
+++ includes/menu.inc	22 Mar 2009 20:48:47 -0000
@@ -1727,7 +1727,6 @@ function _menu_navigation_links_rebuild(
   $menu_links = array();
   foreach ($menu as $path => $item) {
     if ($item['_visible']) {
-      $item = _menu_link_build($item);
       $menu_links[$path] = $item;
       $sort[$path] = $item['_number_parts'];
     }
@@ -1737,7 +1736,7 @@ function _menu_navigation_links_rebuild(
     array_multisort($sort, SORT_NUMERIC, $menu_links);
 
     foreach ($menu_links as $item) {
-      $existing_item = db_fetch_array(db_query("SELECT mlid, menu_name, plid, customized, has_children, updated FROM {menu_links} WHERE link_path = '%s' AND module = '%s'", $item['link_path'], 'system'));
+      $existing_item = db_fetch_array(db_query("SELECT mlid, menu_name, plid, customized, has_children, updated FROM {menu_links} WHERE link_path = '%s' AND module = '%s'", $item['path'], 'system'));
       if ($existing_item) {
         $item['mlid'] = $existing_item['mlid'];
         // A change in hook_menu may move the link to a different menu
@@ -1745,10 +1744,15 @@ function _menu_navigation_links_rebuild(
           $item['menu_name'] = $existing_item['menu_name'];
           $item['plid'] = $existing_item['plid'];
         }
+        else {
+          // If it moved, put it at the top level in the new menu.
+          $item['plid'] = 0;
+        }
         $item['has_children'] = $existing_item['has_children'];
         $item['updated'] = $existing_item['updated'];
       }
       if (!$existing_item || !$existing_item['customized']) {
+        $item = _menu_link_build($item);
         menu_link_save($item);
       }
     }