I have the same situation.
Just installed 6.01 custom ISO and then installed SpamAssassin. Install went fine, and the first e-mail I sent through showed the SpamAssassin headers. Since then, however, there is no indication SpamAssassin is running.
I had exactly the same situation with the 6.01-01 ISO from contribs. org -- installed SA, saw the headers in one message, then never again.
I went looking for the SA log and found /var/log/sa/sa24, but it appears to be a binary file, not text. A clue perhaps?
Robert
Robert