If you run two servers from the same IP address, they must each have different port numbers. They will both show up and players can connect to both if all ports are properly forwarded assuming you are using a router.
If your machine has plenty of power behind it, the safest way to run multiple servers from the same machine is to virtualize it. Since your obviously running Windows, download Microsoft Virtual Server 2005 R2 and you'll be good to go! There is no charge to license MSVSS now thanks to increased competition.
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