Can you advise what wires your referring to, and what wires are connected to what terminals.
You will see on page 9 of the install manual here, what the wiring configurations should be, the key for hot water is there should be something going to terminals 1 and 2.
The wire colours you reference are not a standard, however there will be two cables which will be the mains feed (to power the timer), which would go to the N and L terminals
This then leaves 3 other wires.
Two should be switched lives, which will result in the boiler being called for heat and the valve actuator moving to control the flow for CH or HW.
The remaining wire will be the constant live which makes up the other side of the switched circuit, however if you have a room thermostat this may also be what one of the pair of wires relates to.
Once I know your terminal layout, and what colours go to terminals 1 and 2 we can troubleshoot further.
Please let me know if I can be of any further assistance.