Puzzlebobble indicated a by pass was not needed if a 3 port valve was fitted, ( and it isn't).
Also a 3 port valve means the pump has a role to play with HW side as well as the CH side, but the 3 port valve can't be part of the problem.
That aside, my opinion is the PCB is a monitoring device and when it goes to 'lock out' it indicates there's something wrong and it will not allow the boiler to be re-lit until the fault is corrected.
As you have found, it can be re-lit so at that moment in time there was no fault. Otherwise it wouldn't start.
But the problem keeps re occurring and eventually the culprit is found to be the monitoring device itself.ie the PCB.
This was a real problem 3 or 4 years ago as I mentioned and many PCBs when examined closely with magnifying glass revealed 'dry joints' and hair line cracks where the terminal posts were soldered.
I had to pay for a new version of the PCB and since then there's a 3rd version.
I understand the last version includes the connecting wires already attached to the PCB to prevent damage at the connecting points.
The symptons do equate with the PCB problem and it's not just the HW side as was first thought.
Best thing is to call potterton and see what's on offer.