If you are using the same IP to host two domains, each with a separate certificate, then only one certificate can be default and associated with that IP when SNI is not enabled. NGINX is probably choosing one of your two domains to be "default" (if you haven't set it up that way explicitly). What happens when you hit the server without any domain (i.e. via IP address in the browser)? Is the site you see the one that got the A+?

SNI is what allows you to use two different certificates (associated with two different domain names) with the same IP address. Your choices seem to be:

1. Rely on SNI, which doesn't work with IE on WinXP, or on 2.x Android;

2. Give your server two public IPs, with each pointing to a different domain; OR

3. Generate a single SAN certificate that references both domains (http://en.wikipedia.org/wiki/SubjectAltName) Not all certificate issuers can generate a SAN certificate.