One big thing i would do if i were you is not use a windows 2000 pre sp1 cd to upgrade. make sure the disk has sp1 intergrated in to it. If not your DC's may not pick up the full compter name correctly. Ex. svr1.dns.com
If it does not change the full computer name properly you will have a lot...
I had the same problem. This is caused by upgrading with a windows 2000 disk pre sp1. Below is the link to fix this problem from microsoft. Do the registry hack from the page then restart the server and it should work correctly.
http://support.microsoft.com/default.aspx?scid=kb;EN-US;257623
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