diff --git modules/system/system.admin.inc modules/system/system.admin.inc
index 0b6e456..97bcf29 100644
--- modules/system/system.admin.inc
+++ modules/system/system.admin.inc
@@ -1729,13 +1729,18 @@ function system_clear_page_cache_submit($form, &$form_state) {
  * @see system_settings_form()
  */
 function system_file_system_settings() {
+  
+  $form = array(
+    '#validate' => array('system_file_system_settings_validate'),
+    '#submit' => array('system_file_system_settings_submit'),
+  );
+  
   $form['file_public_path'] = array(
     '#type' => 'textfield',
     '#title' => t('Public file system path'),
     '#default_value' => variable_get('file_public_path', conf_path() . '/files'),
     '#maxlength' => 255,
     '#description' => t('A local file system path where public files will be stored. This directory must exist and be writable by Drupal. This directory must be relative to the Drupal installation directory and be accessible over the web.'),
-    '#after_build' => array('system_check_directory'),
   );
 
   $form['file_private_path'] = array(
@@ -1744,7 +1749,6 @@ function system_file_system_settings() {
     '#default_value' => variable_get('file_private_path', ''),
     '#maxlength' => 255,
     '#description' => t('A local file system path where private files will be stored. This directory must exist and be writable by Drupal. This directory should not be accessible over the web.'),
-    '#after_build' => array('system_check_directory'),
   );
 
   $form['file_temporary_path'] = array(
@@ -1753,7 +1757,6 @@ function system_file_system_settings() {
     '#default_value' => variable_get('file_temporary_path', file_directory_temp()),
     '#maxlength' => 255,
     '#description' => t('A local file system path where temporary files will be stored. This directory should not be accessible over the web.'),
-    '#after_build' => array('system_check_directory'),
   );
   // Any visible, writeable wrapper can potentially be used for the files
   // directory, including a remote file system that integrates with a CDN.
@@ -1775,6 +1778,30 @@ function system_file_system_settings() {
 }
 
 /**
+ * Checks that the private and temporary directories do not resolve to the same
+ * directory as the public directory.
+ */
+function system_file_system_settings_validate($form, &$form_state) {
+  $resolved_public_path = realpath($form['file_public_path']['#value']);
+  $resolved_private_path = realpath($form['file_private_path']['#value']);
+  $resolved_temporary_path = realpath($form['file_temporary_path']['#value']);
+
+  if ($resolved_public_path == $resolved_private_path) {
+    form_set_error('file_private_path', t('The private file system path must not be the same as the public file system path.'));
+  }
+
+  if ($resolved_public_path == $resolved_temporary_path) {
+    form_set_error('file_temporary_path', t('The temporary directory must not be the same as the public file system path.'));
+  }
+}
+
+function system_file_system_settings_submit($form, &$form_state) {
+  system_check_directory($form['file_public_path'], FALSE);
+  system_check_directory($form['file_private_path'], TRUE);
+  system_check_directory($form['file_temporary_path'], TRUE);
+}
+
+/**
  * Form builder; Configure site image toolkit usage.
  *
  * @ingroup forms
diff --git modules/system/system.module modules/system/system.module
index a0e5db3..9514426 100644
--- modules/system/system.module
+++ modules/system/system.module
@@ -2096,7 +2096,7 @@ function system_admin_menu_block($item) {
  * @param $form_element
  *   The form element containing the name of the directory to check.
  */
-function system_check_directory($form_element) {
+function system_check_directory($form_element, $private = TRUE) {
   $directory = $form_element['#value'];
   if (strlen($directory) == 0) {
     return $form_element;
@@ -2114,14 +2114,7 @@ function system_check_directory($form_element) {
     watchdog('file system', 'The directory %directory exists but is not writable and could not be made writable.', array('%directory' => $directory), WATCHDOG_ERROR);
   }
   elseif (is_dir($directory)) {
-    if ($form_element['#name'] == 'file_public_path') {
-      // Create public .htaccess file.
-      file_create_htaccess($directory, FALSE);
-    }
-    else {
-      // Create private .htaccess file.
-      file_create_htaccess($directory);
-    }
+    file_create_htaccess($directory, $private);
   }
 
   return $form_element;