Index: includes/menu.inc
===================================================================
RCS file: /cvs/drupal/drupal/includes/menu.inc,v
retrieving revision 1.246
diff -u -p -r1.246 menu.inc
--- includes/menu.inc	10 Jan 2008 20:16:50 -0000	1.246
+++ includes/menu.inc	18 Jan 2008 10:10:13 -0000
@@ -1572,7 +1572,7 @@ function menu_rebuild() {
   variable_del('menu_rebuild_needed');
   menu_cache_clear_all();
   $menu = menu_router_build(TRUE);
-  _menu_navigation_links_rebuild($menu);
+  _menu_navigation_links_rebuild($menu, TRUE);
   // Clear the page and block caches.
   _menu_clear_page_cache();
   if (defined('MAINTENANCE_MODE')) {
@@ -1639,7 +1639,11 @@ function _menu_link_build($item) {
 /**
  * Helper function to build menu links for the items in the menu router.
  */
-function _menu_navigation_links_rebuild($menu) {
+function _menu_navigation_links_rebuild($menu, $reset = FALSE) {
+  // Delete menus that are not active or customized.
+  if ($reset) {
+    db_query('DELETE FROM {menu_links} WHERE customized = 0');
+  }
   // Add normal and suggested items as links.
   $menu_links = array();
   foreach ($menu as $path => $item) {