I think we are confusing terms here.
"New / Recent" posts and "Unread" posts.
New/recent posts can be seen by selecting one of the links above on the second nav bar ie: "Posts Last 2 Days"
"Unread" posts are the ones that are bolded/highlighted and work just like your email client, they will stay bolded until you read or open the thread.
If you want to clear the unread threads then you can do one of 2 things.
1. Open each thread so that it is reset.... not much fun or.
2. On the menu above select Quick Links > Mark Forums Read.
The jist of it is, before we did the upgrade we were using the old way of marking forums as "UnRead".
Most other forums also use this method (cookie based).
Cookie based sucks because it is time based and is not an accurate way to show what threads are unread.
Below is a list of the options, we are now using option 3.
1. Inactivity/Cookie Based (default) - once a user has been inactive for a certain amount of time (the value of the cookie timeout option) all threads and forums are considered read. Individual threads are marked as read within a session via cookies.
This option is how most other forum software and all versions of vBulletin before 3.5 functioned.
2. Database (no automatic forum marking) - this option uses the database to store thread and forum read times. This allows accurate read markers to be kept indefinitely. However, in order for a forum to be marked read when all threads are read, the user must view the list of threads for that forum.
This option is more space and processor intensive than inactivity-based marking.
3. Database (automatic forum marking) - this option is the same as a previous option, but forums are automatically marked as read when the last new thread is read.
This is the most usable option for end users, but most processor intensive.
Dan