diff --git includes/features.menu.inc includes/features.menu.inc
index 8af814b..fa5e705 100644
--- includes/features.menu.inc
+++ includes/features.menu.inc
@@ -257,6 +257,12 @@ function menu_links_features_rebuild_ordered($menu_links, $reset = FALSE) {
             $all_links[$identifier] = $link;
             unset($unordered[$key]);
           }
+          elseif (!empty($parent)) {
+            $ordered[$parent] = 0;
+            $ordered[$identifier] = $ordered[$parent] + 1;
+            $all_links[$identifier] = $link;
+            unset($unordered[$key]);
+          }
         }
       } while (count($unordered) < $current);
     }
@@ -279,6 +285,7 @@ function menu_links_features_rebuild_ordered($menu_links, $reset = FALSE) {
       else {
         $link['plid'] = 0;
       }
+      $link['customized'] = TRUE;
       menu_link_save($link);
     }
   }