Patch by myself. Clear the cache when a theme's settings are saved.

modules/system/system.module

@@ -1077,6 +1077,8 @@ function system_theme_settings_submit($form_id, $form_values) {
     variable_set($key, $form_values);
     drupal_set_message(t('The configuration options have been saved.'));
   }
+
+  cache_clear_all();
 }
 
 /**