I believe that other boards using the same software as us work the same as you are describing that we are working now. We will be upgrading to the new version of our forum software soon though and if the behavior of the way things are marked as read/unread has changed in it you will likely see that change then.
One suggestion is when you open FT you might want to open several windows/tabs with the thread listings of the forums you frequent when you first visit and look them over as you have time then. That way you will have threads marked as read/unread in that window. This isn't for everyone, but works for some. Thanks,