It could have something to do with the new forum.

I would try a couple things.. First would be just to log out and log back in if you haven't already.

Another thing to check is under "User Menu" go to "Edit your Preference" and see what is checked for "Use MARK time stamp feature?" The Mark button allows you to manually mark messages in a forum or the whole board as read. If you want your messages to be marked for you automatically, you should set this value to "No". If you want to manually mark the messages, you should have it set to "Yes". I didn't notice any change since I mark messages manually, but the default value of this field may have changed with the upgrade.