Did you try to symlink base to baseq3 yet?
IIRC, I had to symlink
/home/username/.q3a to
/home/username/.tremulous and within
.tremulous symlink
baseq3 to
base. If you play plain old Quake3 this will cause you problems. Hence, why I ended up implementing Tremulous support in q3map2. Groove, you might want to see if you can get the latest version of q3map2 (either compile it or get the binary from someone). Oh, and let me know what version of q3map2 you have, it will be output when you run the map compiler.
Edit: Well those symlinks are a tad complicated, but it allows you to switch things around easier. In any case,
/home/username/.q3a/baseq3 has to point to
/home/username/.tremulous/base . Of course MacOSX keeps user directories in
/Users (or something like that) instead of
/home .