In popups.module:96 in the function popups_init() there is a condition 

if ($render_mode == 'json/popups') {
  $_SESSION['page_override'] = TRUE;
}

$render_mode is only defined if the condition above about isset($_SERVER['HTTP_X_DRUPAL_RENDER_MODE']) is true, however that is not always the case, and in this case a notice is thrown. 

if (isset($render_mode) && ($render_mode == 'json/popups')) {
  $_SESSION['page_override'] = TRUE;
}

will fix it.