Power to your pump and boiler come from the programmer for heating on through your room thermostat, also from the programmer for hot water on through the cylinder stat.
It also comes from the hot water off connection on the programmer though the cylinder thermostat.
See if the boiler still runs with the fused spur to the programmer off.
If that stops it then try with the power on and the programmer off its base plate
If that stops it then try with the programmer on the backplate and everything turned off
Let me know what you find
Ok, do you know if it is wired like this:
They have 22 designs to choose from!
This is why everybody uses Honeywell....
Like I say, when the programmer is attached and the hot water and heating are off then you will only get power to the permanent live and the cylinder stat through the hot water off connection.
Can you check if that is the only place you have power?
Connection no.2 in the programmer (check the colour of the wire and trace it to the connection box)
Sorry connection no.1
try this diagram
so also grey to the motorised valve and terminal 2 on the cylinder stat
Can you tell me what terminals are live at the programmer when the programmer is off?
It should only be the live
Are there any other wires connected to the live, also in the junction box?
The power to the pump must be coming from somewhere - 9 times out of 10 it is the motorised valve
Ok, and only one of the cylinder stat connections should be live too?
You need to be doing this while the boiler is firing when it shouldn't be
Can you follow the power back from the pump?
This is turning into a nightmare.
Perhaps if you want to spend a couple of hours tracing the cables you can mark them up and then rewire it?
We would then know it was correct and perhaps it will sort any faults?
Without standing in front of it, the only thing I can suggest is following the live to the pump all the way back to the mains and seeing where it gets its power from