can you be a bit more specific?
are you running a dedicated server?
i have a dedicated internet ADSL router PC, that serves the rest of my LAN via internet connection sharing. i have to host games on this machine, or i wont be able to advertise my game on the master server, as quake3(or other) servers wont route through a NAT based network......
the manual explains how to run a NON dedicated server, you just launch multiplayer JK2, goto play, then create server.... towards the bottom of that screen theres an option to change from LAN server or INTERNET server......
and then "bobs ur uncle"