Finally got SpamAssassin working again last night after I upgraded my mail server from debian woody to sarge, and the default behaviour of SpamAssassin changed from write messages back to a mail spool after processing to writing messages out to STDOUT afterwards, not the way I wanted it to work.

After finding this excellent tutorial for adding site-wide spamassassin support to exim 3, and catching a couple of the tweak comments at the bottom of the page, I implemented it on the mail box, and now have full spam trapping coverage again 🙂 Cheers to kyle for the tutorial link!