Ok, I have been working on this for a while but haven't found anything about it. My goal was to use Active Directory Integrated DNS. I have a Forest Root Domain Controller with DNS on it and a Child Domain Controller (New Tree) also with DNS on it. I found some conflicting information on how to install this as there are articles that say to only point the DNS server to itself for the DNS IP properties. Well, if you do that then you can't promote the child to a domain controller unless you have DNS server already setup with the proper zone info. So what I did was installed DNS as standard primary for the zone of the Forest Root on the Forest Root server and DNS standard secondary on the Child server. For the Child Tree zone I setup the zone as standard primary on the Child server and standard secondary on the Root Server. I then made sure both were listed in the name servers tab in DNS properties on both server and enabled zone transfers to only those on the name servers list (also enabled notify to those listed). Then I promoted them to domain controllers (obviously root first) and the DNS zone information was properly transfered to eachother. I had everything replicating and working correctly at this point with no event log errors. At this point I figured it would be ok to change the DNS zones to Active Directory Integrated, so I did so and also had no errors. Problem is that when I add a host entry on one server, it never adds it to the other server. I can force replication and never get any errors what so ever, but it for some reason just decides to ignore that little part about replicating DNS. I've tried it with Secure Updates Only and also without requiring secure updates; still doesn't work. Anyone know why? Maybe I installed it totally wrong but it didn't seem to work any other way.... had many a times where replication didn't work at all, even using the default dcpromo stuff. Seems Microsoft documentation on a new tree with a different DNS name is lacking.
 
I also noticed something else strange, though not sure if this has anything to do with it. Each server changes the Start of Authority entry to itself for every zone, no matter what I put in for it. I figured that the Start of Authority for my Root Domain should be the Root Domain Controller and the Start of the Authority for the Child Tree should be that domain controller. I go in and manually change it on each server, but as soon as I exit and go back to it, each server says it is the Start of Authority for both zones. Please tell me what I'm doing wrong....