Basic pages are being rendered incorrectly do they differ at all to the article or custom content types in any fundamental way?
Is there something fundamentally different to basic pages that explains/ helps me to troubleshoot why the markup is different?


No, content types are completely generic. Drupal core processes them identically, but of course, custom and contrib code can heavily affect how they work.

You're going to need to check your theme, templates and custom modues, and maybe even contrib modules (depending on what you have installed and how you have them configured). The problem is with one or more of them, not with the content type itself.