Why is it taking so long for my house to heat up?
You've bought a programmable thermostat so you can lower the temperature of the house at night, however by doing that you are making it much harder work for the boiler to bring the house back up to temperature. Before your house was at a constant temperature so you boiler would turn on for a bit, off for a bit, on a bit, off a bit over the whole day. Now it goes off for a long time and your house gets cold, then it has to run a very long time to get it back up to temperature again, leading it to overheat and shut down.

It may be your boiler simply doesn't have the grunt to heat your house for that long. Try setting your night-time temperature a bit higher and see if that improves the situation. 

It could also be that your system is gunked up, leading to poor water circulation in your system. Did you have your heating engineer put a cleaner in the system? If not, have him try it.