Sorry, I can't speak for the best way to configure nginx.
But I can tell you that if your paths are incorrect in your configure.php files, you're going to get odd file-not-found messages, and you're going to have session problems with silent unexpected failed logins etc.
I'm wondering if you may also have other issues with your debian setup, depending on which version you're using: http://www.zen-cart.com/forum/showth...ian#post571284



