I have a few weird things with MAIL.
OS 10.3.1 with Mail on Training.
Rules say to delete Junk after 1 day, but mine never does. I have to constantly manally select all and delete.
When I manually flag something as junk in my inbox, it moves message to junk folder, but once there these don't show up as junk colored messages like the rules are set to, even if I select Apply rules menu.