Still no idea what could be wrong, any ideas guys?
No, because I still don't have a clear vision of what you did :)
What criteria did you use when training? did you just train the spam and ham mailboxes that SA generated? or did you hand-sort prior to training?
If you just trained SA based on it's previous classifications without any hand sorting, why would you expect any sort of change at all?
Are the BAYES_* rules showing up in the Spam-Status headers of the messages in the second run? What's the mix like?
Try gathering some bayes-specific stats using grep: I'd suggest looking at bayes 00, 50, and 99 to start with.
grep BAYES_00 spam.mbox |wc -l
grep BAYES_50 spam.mbox |wc -l
grep BAYES_99 spam.mbox |wc -l grep BAYES_00 ham.mbox |wc -l
grep BAYES_50 ham.mbox |wc -l
grep BAYES_99 ham.mbox |wc -lCompare those to the total counts of each mailbox.
