The past few days I am also losing the new message flags. I will login, it shows there are new messages in multiple forums. When I go into one folder then all folders get marked as read. But I didn't read all the messages.
I noticed that happens sometimes as well. Not to worry, I have transferred the site to another company, it should take effect later this week. I'm using the time to upgrade us to the latest versions, everything should be nice in the future.