I had a similar problem with a 100% new bike with Sugino Zen Chainring, EAI cog, and Izumi ESH chain, all 1/8". It was loud and rough, despite good chain tension, good chainline, and meticulous chain maintenence. It never got any better no matter how much I messed with it, and thankfully the cursed Izumi chain wore out after 420 miles. I tried it with a Surly cog as well and it was so loud and rough that it was basically unrideable. NJS my ass! Never again! I put a cheapass KMC chain on and it has been absolutely silent ever since.

Edit: heres the thread I started about it. http://www.bikeforums.net/showthread.php?t=249091