Problem with table schema
Figured it out. It had to do with using MultiSite apparently when you use multisite and bootstrap it will only bootstrap to the main site. I found an article talking about it here https://drupal.org/node/2080819

Basically you need to override what the system variable is for the url so that it will bootstrap to the correct site.

define('DRUPAL_ROOT', '/path/to/drupal');
require_once DRUPAL_ROOT . '/includes/bootstrap.inc';
$variables['url'] = 'http://subsite1.example.com/';
drupal_override_server_variables($variables);
drupal_bootstrap(DRUPAL_BOOTSTRAP_FULL);