If I don't use sa-learn manually, how is sa supposed to be made aware of its degree of non-success (the false negatives)?
It can't.
Autolearning isn't a perfect solution, it just provides a reasonable mechanism where some learning can occur without manual effort. You should still be training it using sa-learn whenever practical, especially when it has false positives and negatives, and very especially when the BAYES_ rule that matched is on the wrong side of the center line (50).
However, just because the bayes engine doesn't learn one message, doesn't mean it can't learn from other messages and be able to correctly catch it next time. Remember.. bayes doesn't learn a message.. it learns the substrings in a message, which may be the same as some of the substrings in the message that got missed before... So don't over-obsess about training every single false negative.
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