vhost.conf.master placed in /root overrides vhost.conf.master in ispconfig/server/conf
A vhost.conf.master placed in /root overrides vhost.conf.master in /usr/local/ispconfig/server/conf
This drove me crazy because I made a backup of /usr/local/ispconfig/server/conf-custom/vhost.conf.master and removed it and it's settings still were applied.