I used ee to install nginx and WPMU with subdomain support. WPMU works properly. The primary domain works (domain1.org), and the secondary site works on the subdomain (site2.domain1.org).
When going to the secondary domain (domain2.org) I see the “Welcome to nginx” page. When I configure WPMU to use domain2.org, the welcome page remains.
This is the second WPMU VPS server I have setup, the first one works flawlessly. Both times I used ee. I have compared the sites-available configs and they are identical (except for the domains). “server_name_in_redirect off;” was commented out on the problem site so I uncommented it, reloaded the nginx config, with no change, so I restarted the server, and still no change.
Here are my two sites-available config files, but as I said I am pretty sure they are identical.
http://pastebin.com/VQVdLygF
http://pastebin.com/ChwwD2Y