I had actually checked the Scope Management section earlier to see and what happens is if I remove both domains, then add one in, it looks fine in the scope management(however they are all listed as the FQDN of the domain not the Pre-Win2k). When I attempt to add the second domain in a different management group, even though it gives me an error and doesn't seem to make any changes, the Scope Management shows details of the second domain I went to add in the first domains AD FQDN details. So it somewhat mixes up both domain data into one AD Domain.
I'm not sure if I'm painting the picture properly here with my post but perhaps I'll start adding some screenshots.