diff --git includes/module.inc includes/module.inc
index 40396b1..a4ba61f 100644
--- includes/module.inc
+++ includes/module.inc
@@ -927,6 +927,13 @@ function drupal_alter($type, &$data, &$context1 = NULL, &$context2 = NULL) {
     // initialized.
     global $theme, $base_theme_info;
     if (isset($theme)) {
+      // Do not run THEME_form_system_theme_settings_alter as we've already
+      // called it in system_theme_settings to generate the form and calling
+      // it again would incorrectly populate the form with the admin theme
+      // values.
+      if (isset($extra_types)) {
+        $extra_types = array_diff($extra_types, array('form_system_theme_settings'));
+      }
       $theme_keys = array();
       foreach ($base_theme_info as $base) {
         $theme_keys[] = $base->name;