After reading a thread, and navigating away, the thread remains marked as unread. Not sure if this is indefinite, but for right now it seems as if the only way to quickly and conveniently mark them as read is to use the board or section-wide Mark as Read tool, which could lead to potentially missing out on threads accidentally.
I believe it marks threads as read/unread based on your last visit time and the threads last update time, with no account for individual threads. I'll look into adding something that tracks visits through threads, shouldn't be terribly complicated.
With how it does the read/unread calc, it should also be pretty easy for me to add a "View threads updated between" feature so people can get 'new' posts from certain date ranges.