Your fan may not be slow running when there is no demand. This causes the pilot to suffocate after a while. A tell tale sign is the lack of any fan noise (can be very quiet) when there is no demand, and the top of the boiler being warm after a period of no demand.
Likely causes are a dry joint on the metal clad slow run dropper resistor, or a broken flow microswitch. Try operating the flow microswitch with your finger, it should have positive clicky operation like the DHW microswitch. Check for AC volts (careful, mains voltage) across the leads going to the fan when there is no demand.
c
March 2008