You haven't really given any information to help diagnose a fault, but my first choice would be to examine the three port valve for correct operation. That is if you have one.
maybe it's the boiler pcb faulty running it's anti pump seize mode. some boilers will run the pump every 24 hours if the boiler hasn't operated. if the pcb is faulty it might not recognise that the boiler has been on so operates the pump at the same time every night. i've had this problem on a potterton suprima before.
Its a Worcester Bosch Condensing Boiler 3 years old, they (my service provider) say there is a faulty circuit board, so some relays are not opening/closing properly, they are to replace that next week so we shall see if that sorts it.
