sorry, but is still can't understand why it is problem and what for you need to mark everything ?

When user click "mark all forums read" all forums become not highlighted ("no new messages in forum" icon), and i can't see why you need to lose all read-not read information for all threads in all forums? In any way each user may set highliting time to for example to 1 hour in his user CP and all threads older then 1 hour will have "read" highlight