Domain issue

I currently have WP running on my primary domain under http://www.domain.com/news. The problem I have is when visitors coming to my News page from a twitter feed or any outside link cannot get to my primary domain webpage when clicking “home”. It takes them to the News page only. I can change this under “settings” if I make Site Address my domain home. When I do this, clicking on “leave a comment” or the article title itself take the reader to my domain home page. They cannot leave a comment or open the article by itself. Frustrating. Am I doing something wrong?