As we all know running SQL server on a non-standard port can help improve security. What makes the matter a little difficult is that on Windows x64, SQL Server 2000's Client Network Utility doesn't work quite as it should. Any aliases that you create in there will not be picked up by enterprise manager or any other tool that uses the libraries.

In order to get around this problem, you need to use the client network utility from c:\windowsfolder\syswow64 (replace windowsfolder with the name of the folder where windows is installed, such as c:\winnt or c:\windows)

You can also update the the Program menu's shortcut to point to cliconfg.exe that's located in C:\windowsfolder\SysWOW64\

Now it will make the proper registry entries and the programs that depend on it will work.