Lots of things could cause that, leaky duct like you said, poor insulation or air sealing in the ceiling by the register, or an uneven airflow situation.
I had a sharp guy explain to me that AC's are also dehumidifiers and the reason you don't want one to be oversized is it will cool too fast and cut off before it has the chance to dehumidify the air. I would assume that is not an issue since the house is new construction, it was hopefully sized properly.
Do you have one centralized return for the system in question or returns in every room? If it's centralized and the registers getting mold are behind closed doors, it could be that the air isn't circulating. I had a unit replaced about 5 years ago and they explained this to me and talked me into spending a few hundred extra bucks to add a return to all of the bedrooms and boy it was a game changer. The house became way more balanced in temp instead of the variations in temps in the bedrooms I always blamed on being on the "sunny side" of the house.
If you don't have one, you can pickup an infrared thermometer for $25 or so on amazon. With the ac off you can shoot the ceiling around all your registers and if the two getting mold are hotter/colder than the others, you likely have an airsealing/insulation issue. You can also see if those 2 registers are just blowing colder/warmer air when it's cut on.
That's all I have for you. There are some professional HVAC guys on the board that can probably tell you a lot more.
As an ETA. I am getting a whole house ductless mini split system installed on Thursday and I am geeked about it.
2nd eta. Looks like everyone of us know-it-alls want you to check that ceiling temp around the registers, lol.