When I first set up the junkmail accounts on MacOS X Server, I came across some web pages describing problems that people had been having with it. Details are also given here: http://wiki.apache.org/spamassassin/SpamAssassin_on_Mac_OS_X_Server
Probably the most visible problem was that the spamassassin configuration file supplied used obsolete keywords, from a previous version. This is /etc/mail/spamassassin/local.cf. Run spamassassin –lint to see the errors in this configuration file.
But the second problem took some time to become obvious. The spam filter on the server seemed substandard in recognising spam, and didn’t seem to learn as more spam was sent to the junkmail account. The reason was that, although the nightly cron job was processing the spam, it wasn’t being written to the right directory! The two folders involved are /var/amavis/.spamassassin and /var/clamav/.spamassassin. Just make one into a link to the other to fix this problem (it obviously doesn’t matter which one is which).