The boiler switched on but did not fire (maybe the HW cylinder is already too warm?)
I am getting blue in the face trying to tell you issue has 99% probability nothing wrong with the what you are looking at
System operation.
Timer switches on to call for heat ( boiler has not seen a demand at this moment in time )
Neither thermostat is calling for heat therefore………( boiler has not seen a demand at this moment in time )
Sometime later HW thermostat calls for heat - now there is demand for heat at the boiler
OR
CH thermostat calls for heat -( boiler has not seen a demand at this moment in time )
Motorised valve moves to close HW port - only now will the boiler get out of bed to get on with the task
Fandyman, the repair of what is happening is a task that will need professional assistance.
What you are trying to comprehend at this moment in time is beyond your reach. Do not be offended, I am not being rude, just realistic.
Some salient points for you are 1. Boiler will not run unless the orange wire on the 3 port is at mains voltage. Forget the rest as it will just muddy the water for you.
2. if now the boiler is firing with pump not running, another fault has been introduced.
3 my money is fault that you originally posted is within the boiler.
4. What you post is being looked at by all the posters who do not have visual of what you are looking at and lot of what you are posting is not relevant
5 fault diagnostics is the only way to get to the bottom of this saga. You appear not to have the tools or the knowhow to do this. Please do not be offended