Sometimes Spam Assassin dies and needs to be restarted by cPanel or an admin if cPanel is flaking out. I've never seen it flag something as Spam and have it get by the filter though, that part doesn't seem possible to me, but hey, anythings possible I am told.

It really depends on the server. If you want, open a support ticket and we will have a look at it. We'd need an example email with all headers attached to your ticket so we can see the relevant information.