? sites/default/files
? sites/default/settings.php
Index: modules/system/system.admin.inc
===================================================================
RCS file: /cvs/drupal/drupal/modules/system/system.admin.inc,v
retrieving revision 1.327
diff -u -p -r1.327 system.admin.inc
--- modules/system/system.admin.inc	4 Jan 2011 04:02:29 -0000	1.327
+++ modules/system/system.admin.inc	7 Jan 2011 18:46:43 -0000
@@ -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',