--- modules/system/system.admin.inc	2010-11-28 16:31:05.000000000 +0100
+++ modules/system/system.admin.inc	2010-11-28 16:36:42.000000000 +0100
@@ -467,7 +467,7 @@ function system_theme_settings($form, &$
     // If $logo_path is a public:// URI, display the path relative to the files
     // directory; stream wrappers are not end-user friendly.
     if (file_uri_scheme($logo_path) == 'public') {
-      $logo_path = file_uri_target($logo_path);
+      $logo_path = variable_get('file_public_path', conf_path() . '/files/') . file_uri_target($logo_path);
     }
     $form['logo']['settings']['logo_path'] = array(
       '#type' => 'textfield',