--- privatemsg.module	2011-04-22 17:41:43.000000000 +0200
+++ privatemsgNew.module	2011-04-22 17:34:53.000000000 +0200
@@ -2320,12 +2320,14 @@ function privatemsg_privatemsg_thread_op
  */
 function privatemsg_popups() {
   if (variable_get('privatemsg_popups', TRUE)) {
+    $url_prefix = variable_get('privatemsg_url_prefix', 'messages');
     return array(
       '*' => array(
-        'a[href*=messages/new]' // Write new message
+        'a[href*=' . $url_prefix . '/new]' // Write new message
       ),
     );
   }
+  
 }
 
 /**