Investigating this in the support ticket, will update this post accordingly when we find the root cause.
Not 100% sure but are there any files under /home/yellowtent/boxdata/mail/spamd/<mailboxname> ? Those are the per mailbox spamassassin bayes databases. Maybe it's picking up something from there?
Did anything come of this...?
(still an issue - also possibly related to https://forum.cloudron.io/topic/4921/bayes_00-rule-set-for-some-mail-to-mailing-list-no-mailbox/1 ?)