I have been having the exact same problem. I took it back to the shop where I bought it and they said it was normal for fixies to have some chain noise. I didnt buy that so I went for a second opinion at the shop where I go if I do need work done to my other bikes. They told me that the #1 thing I could do was change the chain for a better quality one. The chain that came on the bike from the factory was about a $10 chain. I paid $40 for a Dura Ace chain and that quieted it down greatly.
It still has a slight amount of sound. Nothing like it did before. I will ride it for a month or so now and see where it is then.