Many MUAs tag SPAM themselves and move SPAM to a junk folder (Thunderbird uses "Junk").
It is said to not automatically train these mails, but let have an human revise them.
I really think you should turn that off. When it eventually does classify email, you will run into problems because you have two spam filters fighting over control.
Currently, I have configured those folders as "trash" folders for antispam, which means that those messages are essentially lost, because a move into a spam folder will not train them. -> The current antispam plugin ignores moves in and out of trash folders completely. I wonder why the move trash -> SPAM is ignored?
Mostly because you could hit "undelete" and afaiu it would put them back? I haven't ever really used trash folders, somebody else requested support for those.
johannes