Nevermind. Resolved this by hacking the code.
meta-descriptions.php:107
$desc = str_replace(
> array(‘{excerpt::autogen}’, ‘{excerpt}’)
> , array($auto_excerpt, strip_tags($post->post_excerpt))
> , $format);
$post->post_excerpt is set to ”, and as it is the last value in the replacement array it takes a higher priority than $auto_excerpt (which is correctly set).