Hi, about a week ago I upgraded to SA 3.0.0 from 2.64. I run spamd (with options "-d -c"), and call spamc from my .procmailrc. SA is installed systemwide (e.g., local.cf is in /etc/mail/spamassassin), but I also have my own user_prefs file that I tweak.
Is allow_user_rules set in local.cf? If not, spamd is required to ignore your rules in user_prefs, and it's a bug that they are being parsed at all.