It shouldn't - I'm pretty sure that "Mark forum read" will update your read stats with the current time WHEN you click on the link. Perhaps you need to refresh your cache next time you visit the forum?
Next time you're in a forum, check the clock on the upper right - if it's not your current time (assuming you've properly set your time zone), refresh the page and see if things look a bit different.
If you keep having problems, send me a private message or email.
I'm not sure what you mean. Are you regularly marking the forum read? If so, there's already a "Show New Only" link if you're seeing all the messages in a thread - and you're free to edit your profile to show ONLY new messages.