Nginx + Php5-fpm not rendering php files

I believe I ran into exactly the same problem today, nginx does send the request to php-fpm (as indicated in the header) yet you get a 404, even though the file exists and has no (PHP/syntax) error at all, and no errors show up in any log (ngins or php-fpm).

You didn't include your full nginx config, but is it possible you don't have the option "root" define (correctly?) in your "server" section ? You need to make sure you do, that it points to the right location ofc and that it is inside the "server" section, not within a "location" one -- e.g:

server {
    root /var/www/eman;
    location ~ \.php$ {
        fastcgi_pass 127.0.0.1:9000;
        fastcgi_index index.php;
        fastcgi_param SCRIPT_FILENAME /var/www/eman/$fastcgi_script_name;
        include fastcgi_params;
    }
}

If you take a look at the headers http://eman.id.au/test.php responds with then you'll see X-Powered-By: PHP/5.3.2-1ubuntu4.5ppa5~lucid1. It would not show this if the request was not passed to PHP. Also, if PHP cannot find the file path passed to it, it will echo the error No input file specified.

Since your site does output the powered by header and does not have the No input file specified. error the most likely reason is that you have an error in your PHP script and have display errors turned off. This results in a blank page and an entry in your error log, so have a look in there and see if it isn't filling up.