I typically just stayed logged in the FOG, but I logged out to try this.
While I was logged in in read all my replies, then went to to the unread messages list. I read a few that caught my eye, then specifically chose to read the top on and the bottom one on the list. I then logged out of the forum, knowing that the ystem would have flagged me as having read both the oldest and newest 'unread' messages. There were 10 message that remained unread.
When I logged back in, I had no new Replies to threads I had posted in, which is the behavior I would have expected. When I checked unread messages, there were actually 11 of them - the 10 that I intentionally left unread, plus one new one that had gotten posted in the meantime. Again, this is the behavior I would have expected. This was all done using Safari 8.0 on the Mac, btw.
Not sure what to saw about what is going on for you, but it doesn't do that for me?
If it's enough of an irritant that you want to pursue it further, PM me and - with your permission, of course - I could remote into your computer and see if we can figure it out.