I have similar problem. I can get the index.php to display in the document root, but when I type www.mydomain.com/administrator it will not pull the index.php, but if I type www.mydomain.com/administrator/index.php, it will bring the page up. So is this a configuration file issue or a rewrite issue. I need to resolve this due to the fact I have some joomla installs that have a root joomla install and then a subdirectory of joomla installed and I must be able to get the server to respond to the sub-directory index.php files.

I am new to NGINX and let me say it is awesome, but I still have a lot to learn.

Thx
Suttles