Sounds like there is air in the system, and maybe a restriction in a pipe as well?
Sometimes, it is difficult to blead the air out of the high spots.
I've had older hot water heating systems that required weeking bleeding, but they did not make any noise, even with air in the system.
Since its a new home, I wouldn't touch anything. But, I would light a fire under the builders ass to get the problem fixed!
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