Think I just answered this myself. I hadn't seen the "Shared Filters" and "Shared Boards" section in System menu option for Admins. It was when I saw this I realised how the sharing of boards was happening. It was the permissions on the filters that was allowing the boards to be shared either by user type or by project. I was using a filter that I had allowed to be shared with multiple projects without realising it. A simple mistake that I just hadn't spotted.
Hope this perhaps helps someone else that falls into the same trap! All because I was trying to create multiple projects with a high level board and was using the same filter on each project as well at the top level board.
Phew! :)
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