I think this is a really great tool! Especially since it was FREE! I was also having problems with the Log file until I did a SPOTLIGHT search, deleted all files associated w/ JunkMatcher, and did a ReInstall. Worked perfectly, and the Spambayes filter showed up, too. It was "missing" when I tried to install the first time.
You really need to go to their website and TRY to absorb how the filters work (Lots of "techie" stuff). I basically use spambayes because, by itself and with AppleMail's filter system, it does a great job. Sometime too aggressive - just retrain it not to be so aggressive!