The there is something wrong with your wiring!
Are you saying that the timer, boiler, pump and stat are all supplied from the same live feed, or that the boiler, pump and stat were supplied from the timer?
What is timer's CH ON terminal connected to?
There is a standard two core plus earth cable running from the timer/programmer to a double plug socket. The boiler and pump were/are plugged into this socket. The live (red) wire goes to the stat (now the receiver) and returns from the stat/receiver to the double socket where it is connected to the live terminal. Thus when the timer is calling for heat but the stat isnt the boiler remains off. When both controls are calling for heat the boiler kicks in.
I have had to add in a separate blue wire from the N terminal on the receiver to the N terminal in the socket.
I havent opened up the timer but I'm assuming that the timer's CH On terminal is connected to the red wire. Does this make sense?
Chris