Also check if module is in sites/all/modules/contib/pubdlcnt

I think it's fairly common to use site/all/modules/contrib/ for contributed modules, so I suggest adding the following when looking for bootstrap.inc.

if (file_exists('../../../../../includes/bootstrap.inc')) {
  // If this script is in the (drupal-root)/sites/(site)/modules/contrib/pubdlcnt directory
  chdir('../../../../../'); // go to drupal root
}