The editor opens your quark III Arena by loading the correct registry keys that are installed when you install quark III Arena. If you did not install quark III Arena correctly (or are a warezing llama), it cannot find that directory. Solutions: reinstall quark III Arena or stop being lame and buy the game. :]
Soultaker has just finished a new filesystem in preperation of direct opening of pk3 files. All seems to work correctly (no bugs found) but if you do find any bugs, mail Soultaker (soultaker@shader.gamepoint.net) and try to explain what you were doing so he can fix it. :]
Furthermore, you need to extract the .shader files from your pak0.pk3 into "baseq3/scripts/", or install q3radiant which installs these files correctly.