Index: wp-admin/network/site-settings.php
===================================================================
--- wp-admin/network/site-settings.php	(revision 17218)
+++ wp-admin/network/site-settings.php	(working copy)
@@ -55,6 +55,7 @@
 			update_option( $key, stripslashes( $val ), false ); // no need to refresh blog details yet
 		$c++;
 	}
+	update_option( 'rewrite_rules', '' );
 
 	do_action( 'wpmu_update_blog_options' );
 	restore_current_blog();