Murray, I have restructured the directory so we connect at the root level.
I think that is because we define links relative to the document rather
than the root.
Using site/root relative links in your pages cannot affect the way the site is defined. But the way the site is defined can definitely affect the function of your links. An improperly defined site will contain links that never work.
Copy the code for a link that is not working, and paste it here, please.