Spamassassin –lint and spamc return different scores

You always need Spam and Ham samples. By only feeding Spam SpamAssassin refuses to activate the bayesian Spam filter.

By issuing a spamassassin -D < /path/to/a/complete.mail you can check if bayesian filtering is activated or not (somewhere in the whole debug messages).

Hopefully you didn't train SpamAssassin with old Spam (months old). It will only work well if you used recent Spam you (personally or as a company) got in the past. If you don't have Ham or Spam samples right now you should better set SA to autolearn. Then the filter gets trained over time. This takes longer and you can't see the benefit right now, but the outcome will impress you in the end.

Yes, your numbers show the "current" learned messages. If these numbers are greater than 200 you are finished. Everything above just makes it "safer" as in "more valid" or "accurate". With auto-learning these numbers will increase over time and also decrease as statistics of old mails will be dropped over time.

The comment Informational: message was not relayed via SMTP implies that the message your scanning has little or no useful header information. Did you by any chance save or export the e-mail message, rather than working on the raw message in your Mailstore?

On testing with some of my higher scoring Spam after removing the Received: headers I get the same informational message and it typically results in a 10 point drop in the score SpamAssassin assigns...