--- template.theme-registry.inc	2008-10-04 11:39:23.000000000 -0400
+++ template.theme-registry_new.inc	2008-10-04 11:39:38.000000000 -0400
@@ -59,7 +59,7 @@ function _zen_theme(&$existing, $type, $
   zen_theme_get_default_settings($theme);
 
   // If we are auto-rebuilding the theme registry, warn about feature.
-  if (theme_get_setting('zen_rebuild_registry')) {
+  if (theme_get_setting('zen_rebuild_registry') && $theme == $GLOBALS['theme']) {
     drupal_set_message(t('The theme registry has been rebuilt. <a href="!link">Turn off</a> this feature on production websites.', array('!link' => base_path() . 'admin/build/themes/settings/' . $GLOBALS['theme'])), 'warning');
   }