--- modules/system/system.admin.inc.orig	2009-12-17 15:10:19.000000000 +0200
+++ modules/system/system.admin.inc	2009-12-18 10:32:16.000000000 +0200
@@ -1135,8 +1135,9 @@ function system_modules_submit($form, &$
     foreach ($new_modules as $key => $module) {
       if (!drupal_check_module($module)) {
         unset($new_modules[$key]);
+      } else {
+	$sort[$module] = $files[$module]->sort;
       }
-      $sort[$module] = $files[$module]->sort;
     }
     array_multisort($sort, $new_modules);
     drupal_install_modules($new_modules);