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Your Windows 2000 Professional boxes will try to register themselves with the IP address that the computer recognizes for DNS resolution. To stop your Win2k Pro boxes from hitting your non-Win2k DNS boxes with DNS registration packets, simply go to the properties of your NIC, select "TCP/IP" properties, and hit the "Advanced" button. Select the "DNS" tab and uncheck the "Register this connection's address in DNS."
This will stop the packets that hit the non-Win2k DNS box.