root should also change when cloning site.

platform/clone.provision.inc

@@ -42,6 +42,7 @@ function drush_provision_drupal_provision_clone($new_uri, $platform = null) {
   $options['uri'] = ltrim($new_uri, '@');
   $options['name'] = $new_uri;
   $options['platform'] = (isset($platform)) ? $platform : $options['platform'];
+  $options['root'] = d($options['platform'])->root;
   $options['aliases'] = array();
   $options['redirection'] = 0;