As far as I can tell, q3map2GUI is borked. What I found to be a good solution, if your version of radiant is lacking build menu options, is to set up a few scripts that pass the apropriate values to q3map2. The absolutely vital ones are -fs_basepath and -fs_game.
NOTE:
The q3map2 executable is likely named "q3map2.ppc".
NOTE2:
I do NOT have access to the computer where I set this while writing this post.