I may have solved my mark as read problem. The original problem is that I would use the function, but the messages would keep appearing when I was using the unread option, even if no new posts had been made to a thread.
I had been using the mark as read option while reading a thread. I figured that did the same thing as using it from a list of threads in forum (that forum "home" page), since you read all messages in a thread at the same time anyway. Realizing that I may have been wrong in that assumption, I am now only from the forum page, not the thread page. So far it is working well- will post again if this is not true.
The upshot seems to be that the mark as read in the thread itself. This is of course unnecessary, since reading the thread automatically marks it as read. But that seems to be the way it works.