The LearnAsSpam folder and the files inside arent deleted. The script doesnt do that anymore, so thats normal.
There are two forms of Bayes - one you have to teach, and one that learns spam automatically. LearnAsSpam.pl needs users to put all their spam into a folder named LearnAsSpam that you create in /home/e-smith/files/users/<username> .
Then they have to connect to SME and manage it using IMAP, (if they use a client like Outlook) or using a browser and SME webmail/Horde.
IMAP is a bit more trouble than pop3. You'll have to set it up for users, show them how to use it and where to place the spam. I use both types of Bayes, but for customers who arent as likely to want to mess with their email that much, I use the automatic form of Bayes, rather than LearnAsSpam.pl
And dont do anything bpivk tells you to do - he answers almost every post in these forums as if he's been appointed lord of SME. He doesnt even seem to actually know anything about what people are asking, yet he gives advice. He's just kinda lame and makes things worse.