diff --git a/modules/system/system.module b/modules/system/system.module
index 6537671..a0e94fc 100644
--- a/modules/system/system.module
+++ b/modules/system/system.module
@@ -2751,10 +2751,13 @@ function system_settings_form_submit($form, &$form_state) {
   form_state_values_clean($form_state);
 
   foreach ($form_state['values'] as $key => $value) {
-    if (is_array($value) && isset($form_state['values']['array_filter'])) {
-      $value = array_keys(array_filter($value));
+    // Skip saving array_filter as variable.
+    if ($key != 'array_filter') {
+      if (is_array($value) && isset($form_state['values']['array_filter'])) {
+        $value = array_keys(array_filter($value));
+      }
+      variable_set($key, $value);
     }
-    variable_set($key, $value);
   }
 
   drupal_set_message(t('The configuration options have been saved.'));