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I get the idea from struggling with a similar problem (Domino 8 on Windows 2008 64 bit) that multiple IP addresses and ports make things confused between the server console, the server controller and domino. Another possible IP issue to look for is if DHCP is running.
Here is an IBM technote with a workaround for a similar problem. Title: "
Unable to start the Domino 852 server as a service and run the Java Controller on Windows 2008 R2 server"