I have a Vaillant boiler that clunks when it is heating. I have checked for trapped air in the system and can’t seem to get this thing to quit clunking. It is 7 years old and has an expansion tank on the system with an automatic bleeder. I have manually checked it to make sure the bleeder is working correctly, I bleed the radiators a couple times a year.
Clunking often occurs in boilers with small quantities of water held inside the boiler. In spots where water flows too slowly, the water turns to steam bubbles, then the bubbles collapse when they mix with cooler water, making the clunk.
This will happen more frequently in multi-zone systems when only one zone valve is open, so the water flow in the boiler is restricted. the solution may be to install a 1/2-inch bypass from the pump to the other side of the boiler to insure an adequate minimum flow through the boiler.
Another possibility is a clunk from the closing of a Honeywell zone valve. There are other locations to move the valve or to use another make of zone valve.