I have a Monitor MZ25C combi boiler with an indirect water heater. Here's my problem...when water heater water temperature falls naturally, meaning nobody is using water but the water in the tank is just cooling off after sitting for a long period of time, the magnetic zone valve will open, the boiler's circulator pump will kick on and the boiler will fire as it should. When the water temp in the water tank reaches the set level (120 degrees after about 2-3 minutes), the zone valve will shut and the circulator and boiler firing will also cease at the same time. The issue is that when the zone valve, fire and circulator all shut down at the same time, there is a thudding noise followed by a series of smaller thuds and the pressure indicator on the boiler jumps up and down a few PSIG.

This noise doesn't occur when hot water from the hot water tank is being used and new cold water is being introduced to the water heater. In these instances, the boiler water reachs it's high limit and stops firing, but the zone valve and circulator remain open and on. When the water in the tank reaches the set temp, the zone valve closes and circulator stops and there is no noise.

I've owned the house for a year and this didn't start happening until a few weeks ago. Pressure is 1.4 BAR cold and rises to about 2.0 BAR when pump on and water is hot.

overheating and making steam ??
does the boiler circulator pump have different speeds? if so, turn it to a higher speed.

The circulator has a low, med, high setting. It's always been on medium, but I'll flip it to high and see what happens.

Possibly boiling/steam since the water comes to a hault due to the zone valve closing and stopping the circulator flow when the heat exchanger is still very hot. It's a quick series of thuds. Maybe 6-7 and lasts about a second or two. Would it make sense to turn down the temperature control knob on the boiler itself? Right now it's at the highest setting. The range is 68°F to 176°F.

Is that an indirect water heater, or a storage tank? Is there a potable water expansion tank?

Indirect water heater. There is an expansion tank inside the boiler that serves the water heater zone/loop. There's also a seperate expansion tank that serves the heating zones that's outside the boiler.

Generally, an indirect water heater would be used with a standard boiler, not a combi. It has a coil in it, and would be plumbed as a heating zone, that would in turn heat the domestic hot water. A combi boiler has a separate heat exchanger to heat the domestic hot water directly, and if the requirements of the house were met, would not require a tank, of any kind. Often they fall short of meeting the requirements and a storage tank is added to increase hot water capacity. All it needs to be, is a tank, at quite a bit cheaper than an indirect.I'm not quite sure what has been done with your installation, and it would require someone on-site.

The problem was a water logged expansion tank in the boiler that serves the hot water heater loop. Replaced it and now there is no noise. I made a mistake in my post. My boiler is not considered a true "combi" in that it does not serve as a tankless water heater. It feeds a zone loop that heats a indirect water heater.