This has nothing to do with port of entry. There is no reason they can not check your bags to the final destination assuming it's the same airline or one they have an agreement with. It's done all the time.

When you arrive in the us you pick up your bags, clear customs, and drop them off already tagged for their final destination.

Give the flight and airline details and maybe we can come up with a reason, but it's done all the time, bags tagged all the way through, just picked up when you enter and dropped off after customs.