Quick question ??? Do you turn your heat down in the evenings? And from the time you go to bed until you get up how often has the noise been heard?
Hello again (Customer....) Other than "ghosts" I can only think there must be a movement of some sort with the chimney or chimney liner. This would have to be caused by wind but this doesn't make sense either due to the consistency of the pounding noise. The fact that the noise is not there during the daytime is what led me to think about the heat setting being turned down at night having an influence. One thing you should do is keep the thermostat up for a few evenings to see if the noise stops.
You indicated your chimney was inspected. Was this done from the roof and in the attic.? I would suggest making an attic inspection during the time the noise is going on. It should be possible to trace to a specific location the noise is coming from since it is so loud and consistent.
Unfortunately, this is about all I can offer at this point.