I have a similar knocking noise. Our car only has about 400 miles on it though.
I'm guessing it's due to the break in oil that Honda uses. More than likley the lifters are not getting filled properly with oil which in turn is causing alot of chatter in the valve train.
Like gonavy suggests I'd see what it sounds like after you get the engine broken in. I would recommend using Mobil 1 synthetic oil. But that's just me.
