Ok... just got off the phone with support. What happened is that I had virtual hosts that I had since deleted from our DNS servers. So during the upgrade zmproxyconfgen failed leaving the configs in /opt/zimbra/conf/nginx/includes incorrect; along with /opt/zimbra/conf/nginx.conf. When we manually ran /opt/zimbra/bin/zmproxyconfgen it complained about the missing IP:
Exception in thread "main" com.zimbra.common.service.ServiceException: system failure: Cannot find the IP of xxxx.yyyy.zzz.edu
The fix for that was using the management interface, going to domains, and then the virtual hosts tab and removing the unused virtual host(s). If they were actually being used we could've added them to our DNS servers.
Apparently zmproxyconfgen reads the config from ldap, and then uses the templates in /opt/zimbra/conf/nginx/templates/ to generate the config files in /opt/zimbra/conf/nginx/includes
Here's the applicable bug reports:
Bug 66072 – Non resolvable zimbraVirtualHostname prevents upgrade from 6.x.x to 7.x.x Bug 54481 – Can't find included nginx conf file after upgrading to nginx-0.9-zimbra