Index: modules/system/system.admin.inc
===================================================================
--- modules/system/system.admin.inc	(revision 3187)
+++ modules/system/system.admin.inc	(working copy)
@@ -1176,6 +1176,11 @@
   }
   // Validate front page path.
   $item = array('link_path' => $form_state['values']['site_frontpage']);
+  $normal_path = drupal_get_normal_path($item['link_path']);
+  if ($item['link_path'] != $normal_path) {
+    drupal_set_message(t('The menu system stores system paths only, but will use the URL alias for display. %link_path has been stored as %normal_path', array('%link_path' => $item['link_path'], '%normal_path' => $normal_path)));
+    $item['link_path'] = $normal_path;
+  }
   if (!empty($item) && !menu_valid_path($item)) {
     form_set_error('site_frontpage', t("The path '@path' is either invalid or you do not have access to it.", array('@path' => $item['link_path'])));
   }