Ok, I'm nearly ready to roll this out as a production server, just a couple little details left.
OS: Ubuntu 6.06 LTS in Vmware
Looking at the X-Spam-Status headers there is no bayes score (i.e. BAYES_00=-2.599), many other test scores there but no bayes.
Originally used zmtrainsa to feed it around 2,000 spam and 1,000 ham - that works without error.
Blew away the bayes database in /opt/zimbra/amavisd/.spamassassin and fed it another 250 spam and 210 ham, bayes database files were re-created as a result. Ran zmcontrol stop - start, still no score in the headers.
Logs are clean.
Added bayes_path /opt/zimbra/amavisd/.spamassassin/bayes
to /opt/zimbra/conf/salocal.cf.in and ran zmcontrol stop - start. Still no score in the headers.
On my production server (running qmail, vpopmail, spamassassin 2.x, etc) I would run spamassassin -D --lint and get some output but haven't been able to find the equivalent command under zimbra.