I have few installations of spamassassin on FreeBSD. Yesterday I upgraded one of them from ver 3.0.4 to 3.1.0, and now this new version doesn't run as vpopmail user. So when I run spamd -c -d -v -u vpopmail, owner is root, not vpopmail, so It can't write user_prefs in vpopmail home dir.
I upgraded it with portupgrade tool for FreeBSD ports.