Active directory problems upgrading to 2003 server

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I currently have a Windows 2000 SBS server and I am trying to add a new 2003 server to the domain as a DC.I get AD errors when trying to do this caused by Exchange 2000 running on the SBS Server.
There is a utility called ADPREP which you run on the 2000 server but can cause "mangled" results.
Anyone come across this before??

PS This is my first posting so Hi to everyone