Index: src/wp-includes/nav-menu.php
===================================================================
--- src/wp-includes/nav-menu.php	(revision 27345)
+++ src/wp-includes/nav-menu.php	(working copy)
@@ -365,10 +365,6 @@
 
 	$update = 0 != $menu_item_db_id;
 
-	// Only set the menu term if it isn't set to avoid unnecessary wp_get_object_terms()
-	if ( $menu_id && ( ! $update || ! is_object_in_term( $menu_item_db_id, 'nav_menu', (int) $menu->term_id ) ) )
-		$post['tax_input'] = array( 'nav_menu' => array( intval( $menu->term_id ) ) );
-
 	// New menu item. Default is draft status
 	if ( ! $update ) {
 		$post['ID'] = 0;
@@ -376,8 +372,14 @@
 		$menu_item_db_id = wp_insert_post( $post );
 		if ( ! $menu_item_db_id	|| is_wp_error( $menu_item_db_id ) )
 			return $menu_item_db_id;
+
 	}
 
+	// Associate the menu item with the menu term
+	 if ( $menu_id && ( ! $update || ! is_object_in_term( $menu_item_db_id, 'nav_menu', (int) $menu->term_id ) ) ) {
+		wp_set_object_terms( $menu_item_db_id, array( $menu->term_id ), 'nav_menu' );
+	}
+
 	if ( 'custom' == $args['menu-item-type'] ) {
 		$args['menu-item-object-id'] = $menu_item_db_id;
 		$args['menu-item-object'] = 'custom';
Index: tests/phpunit/tests/post/nav-menu.php
===================================================================
--- tests/phpunit/tests/post/nav-menu.php	(revision 27345)
+++ tests/phpunit/tests/post/nav-menu.php	(working copy)
@@ -88,4 +88,32 @@
 		$page_items = wp_get_associated_nav_menu_items( $page_id );
 		$this->assertEqualSets( array(), $page_items );
 	}
+
+	/**
+	 * @ticket 27113
+	 */
+	function test_orphan_nav_menu_item() {
+
+		// Create an orphan nav menu item
+		$custom_item_id = wp_update_nav_menu_item( 0, 0, array(
+			'menu-item-type'      => 'custom',
+			'menu-item-title'     => 'Wordpress.org',
+			'menu-item-link'      => 'http://wordpress.org',
+			'menu-item-status'    => 'publish'
+		) );
+
+		// Confirm it saved properly
+		$custom_item = wp_setup_nav_menu_item( get_post( $custom_item_id ) );
+		$this->assertEquals( 'Wordpress.org', $custom_item->title );
+
+		// Update the orphan with an associated nav menu
+		wp_update_nav_menu_item( $this->menu_id, $custom_item_id, array( 
+			'menu-item-title'     => 'WordPress.org',
+			) );
+		$menu_items = wp_get_nav_menu_items( $this->menu_id );
+		$custom_item = wp_filter_object_list( $menu_items, array( 'db_id' => $custom_item_id ) );
+		$custom_item = array_pop( $custom_item );
+		$this->assertEquals( 'WordPress.org', $custom_item->title );
+
+	}
 }