One of the new methods are used now, it's no longer tracked by cookies.

The new methods cause a performance hit on the server, as I have no idea how much, the least intensive one is used now. This causes the glitch you are facing now.

There is an easy way for each user to fix this glitch, but each user has to do it him/herself. Read the new topics in a forum and then use threadtools in a forum to mark a forum read.

It's also possible to use quick links to mark all forums read.