your in game server browser is probably filtering all the empty and full servers out of the list you're seeing.
Also, qtracker shouldn't be using the promod.bat file to launch the game. qtracker itself creates a command line string on the fly and launches by appending that string to the name of the executable. So, if you try to launch using the promod.bat file, then you'll end up with conflicts. Just have it launch using jk2mp.exe, it'll find the promod directory if you're going into a promod server.