Thanks for the reply. I did actually already do that (plus I removed all the rewrites from .htaccess as a test) - neither made any difference.
If I comment out these lines in seo_class.php:
$link = str_replace('?', '/', $link);
$link = str_replace('&', '/', $link);
$link = str_replace('=', '/', $link);
then the URLs are ok. Why I'm seeing the issue I'm not sure. I can't think of a reason I'd need those three lines with the URL format I want so I think I'm ok