The Problem
The Solution
The problem is that when the cron.php runs, it has not loaded all the modules the same way as the standard [[bootstrap]] and thus the pathauto module may not be loaded before your custom module. The way to solve this is to manually load the important path auto files using a:
function hook_pathauto_bulkupdate() {
include_once(drupal_get_path('module', 'pathauto').'/pathauto.module');
include_once(drupal_get_path('module', 'pathauto').'/pathauto.inc');
// do pathauto_bulkupdate stuff...
}
