We had the same problem and solved it by checking the error.log of our virtual host. We found the following message:
AH00670: Options FollowSymLinks and SymLinksIfOwnerMatch are both off, so the RewriteRule directive is also forbidden due to its similar ability to circumvent directory restrictions : /srv/www/htdocs/wp-intranet/
The solution was to set Options All
and AllowOverride All
in our virtual host config.