Currently, clicking 'next unread' in an unread post will not take you anywhere while clicking 'next unread' in a read post will take you to unread posts that appear after, but not before, that post in the thread. These are quirks that should be fixed in the near future.
Does that describe the issue you're seeing?
Next unread is not advancing to the next thread
Virus and security updates on 10/14/10