I'm not entirely sure that this is the problem you're referring to, but:
If you read one unread board/thread and then press Back, there's a good chance that the browser loads the whole page from cache, instead of getting it again from the server, so you're actually seeing the page in its past state, when you haven't read the said board/thread yet. So, try pressing the Home option in the menu to get the site in its real state.