From what I can tell they've programmed a "timed boost" from 7am to 11pm which is meant to turn on the top element and the boost button is red as if it were activated during those times.
With that set up you want to start by setting up the standard 'economy 7' programme, which refers to the lower element, to come on from 0200 to 0700 (Or whatever period of about 5 hours is safely inside your cheap rate period.) and no timed boost. This should get you a tank full of hot water, enough for about three baths or showers. Use the boost manual or timed if you find that is not enough to last a whole day.
My guess is that the lower element is faulty so someone is decided to use the timed boost as a temporary workaround and never got round to fixing it properly.