Wes,
You picked up on a very interesting topic... one that is debated around all internet forums. Long story short, this is one of those items where there are "fixes" / modifications to alter the "read" post behavior, but they all come with a very high price in forum speed.
There is a new version (1.3) of this forum due out. One item is it will have proper mark as read functionality. Rickard Andersson, the developer of this forum software said (warning... techical content below),
"What I mean by "proper" mark as read functionality is that when you read a topic that has been posted to since your last visit, it will no longer be marked as containing new posts (for that session!). It does not mean that you're "unread" topics are marked as such forever. I can't really think of a situation where you want to save that data for that long. When you are away from a forum for some time and then come back, you're interested in which topics have been posted to. You're not interested in which topics had been posted to the last time you were there.
In short. The only difference between the way it works now and the way it will work in 1.3 is that in 1.3, when you read a topic that was marked as containing "new posts", that indicator will turn off.
There is to my knowledge no fast and elegant way of implementing a long term read/unread posts marking system. Thus, it won't be in PunBB."
adoptedbyachicken is right, this is the way a lot of the forum applications do this. I'm constantly looking for mods / ideas that will work without effecting the speedy response of the forum, but as of right now there isn't anything available.