I have seen several threads on this. There is either no answer or I have implemented the answers (making sure junk mail settings are correct and editing /etc/default/spamassassin).
I have months of training Spamassassin and recieve around 2-300 spam emails a day, all of which I mark as spam. Nothing moves automatically into the Junk folder. Mail only gets into the Junk folder if I amrk it as spam.
It used to work when I was running Ubuntu 11.04. I think it worked in 12.04. Help please!