From Technet article Q198644:
"The error message in not generated by Windows NT Server itself. It originates on the environment's WINS server, which now contains a database entry of for that server. This indicates that the server is registered with WINS and that WINS believes it is a single NIC system, and is, therefore, reporting this as a duplicate name on the network.
To resolve the conflict, add primary and secondary WINS addresses to the second NIC (these should be the same WINS addresses that are listed on the initial NIC), and then restart the system. This will force a reregistration of the system with WINS and the registration will change from UNIQUE to GROUP, and will be labeled Multihomed. The error message will cease. "
So go ahead and configure both adapters to use WINS. It will work better that way.
Here is the URL to the article:
http://support.microsoft.com/default.aspx?scid=%2fsearch%2fviewDoc.aspx%3fdocID%3dKC.Q198644
(please remove any spaces)
Hope this helps.