The problem is located within the Notifications 6.x -2.2 module. Open up /sites/all/modules/notifications/notifications_content/notifications_content.module and comment out lines 847 and 867.

// $tokens['node']['node-url'] = t('The node view url for read more links.');
//        $values['node-url'] = url('node/'. $node->nid, array('absolute' => TRUE)

A patch is also available in the Notifications issue queue.