Well spotted, it should read:
Mail is taking it upon itself to mark messages as read. Its not happening because the messages are being viewed. If you select a message thats second from top and then a few more come in, you can sometimes see the blue dots blink out without any user input at all. The new messages is never selected or viewed.
My MBP is stuttering.
There are no rules set up at all except the default Apple rule(s).