I had the same problem. This weekend I switched out my 16t superbe pro cog for a 19t Surly cog. With the 16t cog, the drivetrain was silent. But with the 19t cog, I could hear that rhythmic grinding sound. I took the bike over to my lbs because I was afraid the chain might be too tight. To accomodate the larger cog I had to move the hub all the way to the front of the dropouts, and there seemed to be a lot of tension on the chain. I figured that was what was causing the noise.

The mechanic at the shop said that the tension and alignment were all spot on. And that actually, 1/8 pitch components can just be noisy. He said it was the sweet sound of success, but that yes, some combinations are quieter than others. He also recounted how the track can get really really loud, and that's it's a very common misconception that track bikes are silent machines.