OK, thanks for the additional info. It looks like I was having a permissions issue and the bayes_* files were not both r/w for users despite having bayes_file_mode set to 0666. I'm thinking probably because the bayes_path was originally created manually with root.

spamassassin reads site-wide config, then users' ~/.spamassassin/user_prefs

spamd can do the same, if it runs under root without the '-x' flag (which
disables this behavior).

spamc connects to spamd passing the username to it, so you can override
current user by passing the "-u username" flag to it.

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