Index: includes/menu.inc
===================================================================
RCS file: /cvs/drupal/drupal/includes/menu.inc,v
retrieving revision 1.413
diff -u -p -r1.413 menu.inc
--- includes/menu.inc	3 Oct 2010 23:29:09 -0000	1.413
+++ includes/menu.inc	7 Oct 2010 04:55:15 -0000
@@ -2890,24 +2890,22 @@ function menu_link_save(&$item) {
     }
   }
 
-  // If we have a parent link ID, we use it to inherit 'menu_name' and 'depth'.
+  // If this link defines a parent link id, try to find it in the current menu
+  // links. If found, we use it for the re-parenting process below. This parent
+  // link validation also needs to be done for links specifying a plid of 0
+  // (zero), since {menu_links} may contain stale/bogus data caused by a
+  // re-parenting process that went wrong in a previous rebuild.
   if (isset($item['plid'])) {
-    if ($item['plid']) {
-      $parent = db_query("SELECT * FROM {menu_links} WHERE mlid = :mlid", array(':mlid' => $item['plid']))->fetchAssoc();
-    }
-    // If the parent link ID is zero, then this link lives at the top-level.
-    else {
-      $parent = FALSE;
-    }
+    $parent = db_query("SELECT * FROM {menu_links} WHERE mlid = :mlid", array(':mlid' => $item['plid']))->fetchAssoc();
   }
-  // Otherwise, try to find a valid parent link for this link.
-  else {
+  // If no plid was specified or it was not found, try to find a new, valid
+  // parent link for this link. Only do this if this is a menu link provided
+  // through hook_menu(). We can not guess the parent for menu items added
+  // through the UI or modules since we can not assume that they are parented
+  // by their path.
+  if (empty($parent) && $item['module'] == 'system') {
     $query = db_select('menu_links');
-    // Only links derived from router items should have module == 'system', and
-    // we want to find the parent even if it's in a different menu.
-    if ($item['module'] == 'system') {
-      $query->condition('module', 'system');
-    }
+    $query->condition('module', 'system');
     // We always respect the link's 'menu_name'; inheritance for router items is
     // ensured in _menu_router_build().
     $query->condition('menu_name', $item['menu_name']);
Index: modules/menu/menu.test
===================================================================
RCS file: /cvs/drupal/drupal/modules/menu/menu.test,v
retrieving revision 1.41
diff -u -p -r1.41 menu.test
--- modules/menu/menu.test	24 Sep 2010 00:37:43 -0000	1.41
+++ modules/menu/menu.test	7 Oct 2010 04:55:16 -0000
@@ -609,7 +609,7 @@ class MenuNodeTestCase extends DrupalWeb
     // Change default parent item to Navigation menu, so we can assert more
     // easily.
     $edit = array(
-      'menu_parent' => 'navigation:0',
+      'menu_parent' => 'main-menu:0',
     );
     $this->drupalPost('admin/structure/types/manage/page', $edit, t('Save content type'));
 
Index: modules/simpletest/tests/upgrade/upgrade.test
===================================================================
RCS file: /cvs/drupal/drupal/modules/simpletest/tests/upgrade/upgrade.test,v
retrieving revision 1.8
diff -u -p -r1.8 upgrade.test
--- modules/simpletest/tests/upgrade/upgrade.test	1 Oct 2010 18:37:22 -0000	1.8
+++ modules/simpletest/tests/upgrade/upgrade.test	7 Oct 2010 04:55:16 -0000
@@ -381,5 +381,9 @@ class BasicUpgradePath extends UpgradePa
     $this->assertText(t('Reports'));
     $this->assertText(t('Structure'));
     $this->assertText(t('Modules'));
+
+    // Confirm that no {menu_links} entry exists for user/autocomplete.
+    $result = db_query('SELECT COUNT(*) FROM {menu_links} WHERE link_path = :user_autocomplete', array(':user_autocomplete' => 'user/autocomplete'))->fetchField();
+    $this->assertFalse($result, t('No {menu_links} entry exists for user/autocomplete'));
   }
 }