[eluser]jedd[/eluser]
An observation.
On the /viewforum/ (thread index) page, where you get the Topic ... (1 , 2) link. If you get that highlighting as having new messages, and then click on the (1) link ONLY .. come back and refresh the thread index page - it shows that that thread is now fully read.
So the CI forums, at least, register any view activity anywhere within a thread as indicating that that thread is now up-to-date, even though the most recent message(s) have not ever been retrieved from the DB for the user.