Посмотрел в логах...
[client localhost] File does not exist: /home/public_html/n, referer: http://localhost/n/

Может первый алиас перетирает нижеследующий?

location / {
root /home/public_html;
index index.html index.htm index.php;
}
location ~ \.php$ {
include fastcgi.conf;
fastcgi_pass 127.0.0.1:11000;
fastcgi_index index.php;
fastcgi_param SCRIPT_FILENAME /home/public_html$fastcgi_script_name;
}
location /n {
root /var/www/html;
include fastcgi.conf;
fastcgi_pass 127.0.0.1:11000;
fastcgi_index index.php;
fastcgi_param SCRIPT_FILENAME /var/www/html/test.php;
}