The code is automatically placed into the .conf file just like it places it in the .htaccess for apache.
I've probably click and unclicked and enabled and disabled every feature twice in the software and my web server. Un ticking and re-ticking the box has no effect, it breaks again when it's checked.
I checked that link. Using their config file instead of mine had no change. All my other rewrites work perfectly fine. Pretty permalinks for example.