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Are you able to check the lver position on the motorised valve for HW only, ch only and both?
When the hot water is satisfied the 3 port valve should then get power from the HW off position on the cylinder thermostat or the clock - are you able to check this if I send a wiring diagram?
Unless the relay is faulty in the motorised valve head and is sticking, keeping the boiler on but diverting the water still to the hot water, hence no heating