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Windows 2000 DC IP and Web Site IP different

Hi, I have a domain with DC of domain.com for the network pointing to one IP, and domain.com for the web site pointing to another.  So i can get the web site to work, I have been deleting the DNS A record for the domain IP that it automatically puts in there.  Then the A record for the web site works.  But then a few days later, the domain IP is back in there again.  Whats the best way to do this?  Is deleting the domain IP bad for our internal network?  Do I have to have the web site for the domain on the same machine as the DC?  Thanks!
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Curtv

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Sounds like madness.  Its no longer in mixed mode, and I'd rather just have IIS on the DC forward to the actual web server if its going to require that much stuff.  I thought I had this set up with our old domain a similar way and never ran into any problems.  Any other ideas?
I don't think you will want to run IIS on a DC. Password protecting part of a website only works with administrator logins and passwords, also windows media services doesn't work with a domain controller, those are the issues I can remember, there maybe others. You could upgrade to windows 2003 server (supports renaming domains).

You could also create a new zone with domain.local or whatever integrate it with active directory then remove the integration with active directory from the old domain. I have not tried this but its an idea. If you do this I hope you have two DCs sync them then take one off line while you try the above.

There is no easy way around this issue. If your going to resolve it, there are many hours of work, but it can be done. I have done it twice in the last year.
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OK well i appreciate the comments.  I will accept your first answer so others can see what to do also.  Thanks!