I got a similiar problem to that. What I did to resolve it was that i put in the Quake III retail cd that I got, then browsed around to find the pak0.pak file (or something similar to that) then copied that over to the pak file in the OSX version that i downloaded and ran the game. worked fine. the downloadable version of quake III doesnt come with the core file you need to run it. you need to get that from the actual Quake III cd.
-tim