Also, it looks like you can use Quick Links > Mark Forums Read to basically reset things as read and start from scratch that way. You would miss a few new ones today if you used the New Posts link; however, you could use Today's Posts to get caught up... then things *should* be accurate moving forward. If they are not, it could be a vBulletin bug, and like I said, we can go back to the old settings... it just sounded like that wasn't accurate either.
As far as invisible mode goes, can someone tell me the steps they used to use to set to invisible and what is missing now. My administrator account is different from yours and my test user account still lets me set myself to invisible in the User Control Panel. I can look into it further as soon as I have a better understanding. Thanks!