I seem to have that problem, too. It will go away, but comes back later saying I have one new message.
Invisible Messages

same here, I have 1 new message that I can't see. Hope that support read this forum, or to send a ticket about it?

When I first go on, it said I had 55 unread messages. I went in an checked, and of course I didn't. I deleted a couple of messages that I really didn't need anymore and after each deletion, the count went down. I think there may be some phantom data in the database that may have been cleaned up after forcing message deletions. Might be worth a try if you have the same issue.

My only guess is that when it says "messages" that it might include responses to message board you've commented in.

My only guess is that when it says "messages" that it might include responses to message board you've commented in.
I'm pretty sure it is just messages in the messaging system and not any other parts of the site. When I really have new messages, it has been populating correctly in the past when I tested the beta out. Today it was all messed up. Still think it might just be some phantom data in the database and a force deletion/update of messages fixed it for me.

I'm not sure where the counter is getting its information. I logged in to one new message, which was legit. I read the message, deleted the message, and instantly got 24 unread non-existent messages.

I just tried sending a message to someone else and for some reason (may have been user error--will have to test again ), it sent to me. I then showed 11 unread messages; had none before. Deleted that one and it said I had 10 unread.
Went and deleted another message I didn't really need, via the checkbox on the main messages page and the delete button and they all went away. So, their is some other problem and not just phantom data.
After the site looks revamp the upper bar claims I have 2 new messages. But when I visit my messages, there are no new messages. I've tried changing the order, clicking on various things, but I still can't see them. Does anybody know what's going on?