For more information:
I changed the following line in /etc/amavis/conf.d/50-user:
$final_spam_destiny = D_PASS;
$final_spam_destiny = D_DISCARD;
then restarted amavis and my server is now blocking spam again, such as:
Mar 29 17:55:53 blacksun amavis: (02593-01) Blocked SPAM, [126.96.36.199] [188.8.131.52] <jeremiah@XXXXX.org> -> <jeremiah@XXXXX.org>, Message-ID: <20090329225551.3E2CCA344@blacksun.XXXXXXXXX.com >, mail_id: NDVWtU6Y74vx, Hits: 31.039, size: 2304, 999 ms
So it appears that the policy setting in ISPConfig are not correctly controlling the flow of spam.