Once you click on Mark Forum read, you can't undo it. It will show new messages after that in red. I use it because I always click on New Posts to see all new posts in all forums since I marked them as read because I don't go to the individual Forums. I find this more efficient for me, I can see all new posts and threads and skip over ones that don't interest me, instead of going to the separate forums.
I think Track Messages is a way to mark threads you're especially interested in, such as when you post a question and want to see replies to it. I'm not sure if you get emailed when there's a new reply, but I think so.
sue- knitting heretic