The problem with two NICs is (as it seems when I did some testing) that usually the game is hosted automatically ONLY local, if I like it or not. On other games others could join my game by IP adress (games that used DirectPlay such as Operation Flashpoint) but dedicated server never was listed in any game browsers.
JK 2 is the first exception where my dedicated was found on the internet even with two NICs. However, my non dedicated game never was found. That was really odd. So if possible, take out one NIC (or disable it, maybe that already helps) and try again. As an alternative, I set up my old 10 Mbit hub again. I lost 100 Mbit between both computers but in return my game is found on the internet now. Maybe you should think about buying a cheap hub, what do you think? At least in Germany 10 Mbit hubs/switches don't cost that much.
The problem by the way seems to be that things like DirectPlay may just take any NIC automatically and usually the wrong one.
I believe there are a very few games where you can select what NIC should be used but that is really rare and not available in JK 2 as far as I know. So as long as you can't select the NIC, that may be the conflict. For my computer it was.
Maybe you should take out one NIC just for testing. At least you know afterwards if that was the problem and if a hub/switch can give you satisfaction.