I am not sure exactly what you do, but I will tell you a couple of things that will affect the marking of items as read.
One is if you leave the forums, even if you keep the same browser window and same site, like if you use the browser window to go to the RR Database, you run the risk of having everything marked as read. This is associated with the way it works if you close the window, it will mark everything as read. (Not really marking it as read, just no longer new.) This sometimes does not happen, but I have yet to figure out why.
Another is the timing issue. I am not sure how this works now, but it used to be if you were browsing the fourms and you left to go get a sandwich and stayed away too long, you would come back and everything was read. Lindsay addressed this before, but that was when it was still the "TrunkedRadio.Net" site, so I am not sure how it is here now.
Hope this helps.