Ok I think I figured it out. There were no problems when my brother on xp hosted the game, but for some reason he couldn't connect to my server, when I tried to host (which seems to replicate your issue).
It turns out that the server can fail to start, but you won't see the error message, because the sequence of commands in the conf file will just go on, clear the screen and start the game.
The issue was probably caused by that it couldn't start on the default port. In your server config file in the IPX section (at the bottom of the file) you should have the command: IPXNET STARTSERVER. Just add a high port number after that. I used 3001, so IPXNET STARTSERVER 3001
There was however a second issue. The client is prompted to type CONNECT <IP ADDRESS OF THE SERVER> <PORT>(note that when you change the port on the server you also have to specify the port on the client when connecting). That didn't work for us. The connect command also has to be prefixed with ipxnet, so: IPXNET CONNECT IP PORT
Let me know if this helped.
P.S. Unfortunately the forum doesn't allow me to upload the conf files directly. I will "docomment" the changes I made in them and upload it tomorrow on dropbox and share the public links here. Feel free to pm me if I forget though ;)
You also have to specify the port even when you use hamachi. I will also mention that when using hamachi the client has to specify the ip that hamachi assigned to the server. You probably know that hamachi has it's own addressing scheme, but there are no obvious things when trying to resolve such problems ;)
And you have to be actually connected over hamachi, there are some sort of rooms/subnetworks - I don't quite remember the hamachi terminology, because I resolved all such problems that I had in the past by purchasing a public ip ;D
Either it's not working for me or I'm misunderstanding you. I've added the port 3001 to the end of the line as you did, (will that port number work for me also?) then when I open client I type in the ip and port of the server, for example: