Had a client report this to me last night, they had created a subserver and then setup an alias server for the sub server. They were unable to get to the website through the alias domain after creating it. I checked it out and sure enough the DNS Server section of the alias server they had setup was bleeding red. I reproduced this on another sub server for another client and have attached the screenshot. What appears to be happening is the DNS information for the primary top level server gets copied into the alias server's DNS file forcing the new domain dns entries to not be loaded.