A friend had something similar, and the problem was the chain routing through the rear derailleur. It was in the wrong side of a metal tab, and each link had to slide over it.
THis seems like a large enough error that it would be obvious, but it isn't. He had taken it for 1-2 mile shakedown rides and the extra drag wasn't so much scream. "wrong wrong", just enough to be noisy.
Something to check...