for quite a while I've been playing with autolearn settings
SA's default is: bayes_auto_learn_threshold_nonspam 0.1 this *can* cause low scored spam to be learnt as ham. For several months I've been using bayes_auto_learn_threshold_nonspam -1.0and so far no more false negatives have been learnt as ham which is was hoping for.
If you're using autolearn, you may want to play with that threshold.. Axb