This is another reason why it was a good idea to have my big application consist of only one public file which can easily be whitelisted. Everything else lives outside the web root and is never directly executed.
Wow, am I glad I caught this link--I'm just now switching my servers from Apache to Nginx/php-fastcgi, configured more or less just like the article says...
I decided to switch to Nginx for the fabled performance benefits and relatively simple configuration. But this now makes me wonder what other gotchas there are in store for me... I have a long history with Apache, maybe I should just stick with it after all...