Magento – New website/store view, all pages 404 (including homepage)

As per the title, I've set up a new store on a different domain and all pages including the home page are returning 404.

I've tried pretty much everything, and I'm wondering if any of you can think of a good way to debug this.

I've tried:

• Clearing Mage cache, reindexing
• Clearing APC cache
• Reloading nginx
• Creating a new CMS page at a certain URL to see if that will load
• Disabling web server rewrites
• Checking store config against other stores that do work (default cms page etc)
• Trying default URLs (e.g. /customer/account)
• Changing the Nginx configuration a few times based on various examples (and also based on the other working Nginx configuration files that are in use)

The site is loading the correct theme, but not finding any content for some reason – it just gives me a 404 page no matter what URL is given.

At this stage, I'm not sure if it is a server config issue or a Magento config issue.

A version is EE 1.12.

Current Nginx conf file is as follows (removed any sensitive variables):

server {
    listen 000.00.000.000:80;
    listen 000.00.000.000:443 ssl;
    server_name subdomain.site.com;
    root /var/www/vhosts/companyname/staging;

#   SSL Configuration redacted

    location / {
        index index.html index.php;
        try_files $uri $uri/ @handler;
#        try_files $uri $uri/ /index.php?q=$uri&$args;
#        expires 30d;
    }
    location @handler {
#        rewrite / /index.php?req=$uri;
        rewrite / /index.php;
    }

    location ~ \.php/ {
        rewrite ^(.*\.php)/ $1 last;
    }

    location ~ \.php$ {
        if (!-e $request_filename) { rewrite / /index.php last; }

#        expires        off;
#        fastcgi_pass   stagebackend;
#        fastcgi_param  HTTPS $fastcgi_https;
#        fastcgi_param  SCRIPT_FILENAME  $document_root$fastcgi_script_name;
#        include        fastcgi_params;

#copied config below

        expires        off;
        fastcgi_pass   stagebackend;
        fastcgi_param  HTTPS $fastcgi_https;
        fastcgi_param  SCRIPT_FILENAME  $document_root$fastcgi_script_name;
        fastcgi_param  MAGE_RUN_CODE site_en;
        fastcgi_param  MAGE_RUN_TYPE website;
        include        fastcgi_params;

#end copied config

    }

}

Relevant settings for the view are (the cms page defined here does exist and is enabled for the storefront):

SEO:

• Web server rewrites: No

Default Pages:

• URL: cms
• CMS Home Page: Home Page
• Default No-Route URL: cms/index/noRoute

Any ideas would be much appreciated!