I had the same problem to an extent. My issue was only with the alignment of the rear wheel in the dropoffs, as the frame was straight, as was the wheel and hub/cog. You'll also have to remember that the sound of the chain engaging with the cogs will make noise, and there's no surefire cure to that. I've also noticed that throughout winter and along with wear, my fixy has become signifigantly louder. Keep an eye on that chain if you ride a whole lot!

Hope this helps.