I will need to address this properly in a future version, but in the meantime, here is a possible workaround:
1. In the function qa_path() in qa-base.php, replace the line:
$paramsextra='';
... with ...
$paramsextra='?qa='.urlencode($request);
2. Later in that same function, remove this line:
.( ($neaturls || empty($request)) ? $request : ('index.php/'.$request) )
3. In qa-index.php, insert the following code:
if (isset($_GET['qa'])) {
$qa_request_parts=explode('/', $_GET['qa']);
$qa_url_depth=1;
}
... before ...
$qa_request=implode('/', $qa_request_parts);
That should do it, but please let me know if it works for you, after testing out all the different functions on your site.