this is a really strange one and difficult to suggest anything without being able to examine the system in person.
i was going to agree with the builders about the frost stat until you said that the boiler isn't fired up.
the only other component thats going to make a noise is the pump, the pump would normally shut down when the programmer switches the system off, although many modern boilers utilise a pump over run stat to dissipate any latent heat from the boilers heat exchanger so perhaps that could be malfunctioning if your boiler has one.
i have come across a system that had a pump that ran constantly but that had been wired up wrongly in the first place, they don't usually start malfunctioning like that of their own accord.
is the pump for your system in the loft? next time you hear the noises during the night see if you can find your pump and and if its running, you shoud be able to feel it vibrating or hear it.
please let us know what your heating engineer finds as its good to know.