I have noticed that if you create a Wordpress page, ie index.html then assign it as the Master Page by checking “This is the master page”.
Then duplicate this page to create another page ie single.html and uncheck the “This is the master page” check box it then un-checks the index.html check box. If you then re-check the index.html to make it the master page it re-checks the single.html page. They appear to be linked so you can’t simply make one page the master page without making all the pages master pages.
Hope this makes sense.