On two different 6.0x servers, spamassassin had ceased to function. I found problems with permissions, the call to spamc, a setuid setting, and bayes/local.cf settings/expansion. I haven't sorted it all out yet but it is working.
On one server, spamc was getting called, with setuid qmailq, but some permissions were wrong on some of the files in /var/qmail (Jesper Knudsen uses more liberal settings then some advise I believe, at least on dcc/map)
On the other server, spamc wasn't getting called (sorry I am not sure how it is supposed to get called yet but spamassassin wasn't touching mmail) so I added into .procamilrc (users folder)
:0 fw
* < 256000
| /usr/bin/spamc -f
and spamassassin began to work, including all other line sin the .procmailrc such as sending to junkmail (I changed it to Junk to align with our email client, and added templates appropriately). From memory I don't recall accurately, but there is an issue with the uid running spamc (spamd, shows in maillog), and/or this is a result of calling spamc this way.
bayes autolearning couldn't access the database, because it wasn't correctly identified in (my) local.cf - at least I'm using a system database in /var/qmail/.spamassassin which should be in the local.cf
bayes_path /var/qmail/.spamassassin/bayes
I hope this mish mash of info helps someone!