I’ve had a problem also, and have been working on this for a few days and no luck. Have tried placing the BBClone code in the header, footer and index file. I’ve even placed it in a ‘bbclone.php’ file within the current theme and used a PHP include with no luck.
Was there a change in how Permalinks work, and could that have ‘broken’ BBClone/WP integration?
May try using the RunPHP plugin and include BBClone that way.