I have ispconfig servers running nginx. When I updated from 3.0.5.3 to 3.0.5.4 I choose to reconfigure services. During this operation, the phpmyadmin links were removed from the nginx config (ispconfig.vhost). I see that there is an apps.vhost on port 8081 that has those apps. I don't remember (actually lost some notes) whether my install is not standard or if this was changed at some point in ispconfig. ispcomm.
phpmyadmin has always been part of the apps vhost, afaik. So I guess you had some non-standard config.
