I have found my own answer and thought I'd share it, in case this happens to anyone else.
My problem was caused in the header with no closing </a> tag after the link markup to our custom banner. It was applying the link to our website, to the entire page, rather than just to the defined banner area.
I don't know why this problem appeared just yesterday, as I have not edited this file for a couple of months. I upload new files nearly each week, and this problem only appeared yesterday?.
Well, I am just happy that it is now fixed.