Years ago I help a friend in uk fix his gas boiler, all the engineers had done the usual board and probe swaps and the actual issue turned out to be the probe was in the wrong place, this unit used a spark gap to ignite the pilot flame and then measured the two wires of the probe and if the tip was not in the flame then it would not heat and shut off the gas, if it was too far forward it would not ignite and too far back it would ignite but the tip would not be in the flame. And the reason it had failed initially was that when they moved in by law a british gas inspector must sign off that the system is safe and when he pulled the ignitor for inspection it was not seated back right.
Of course the usual finger pointing happened and my mate was blamed for the issue at first but then after finding the ignitor was fitted wrong he was able to claim back the fee's.
so if your system has a ignitor style pilot flame control probe that could be the issue.
darkspr1te