Strange occurrence which may have been down to my host playing around and not admitting it, but today when I opened my site and logged in with the account which has host permissions, the authorised site opened inside the modal window. The original site remained open in the main Internet Explorer window.

I edited the web.config to encourage a restart on the server and everything is back to normal after the restart.

I thought it best to post the occurence in case anyone else meets the same situation and needs the solution.