It's an engine sound. Just as Paradox describes, it happens in higher gears under load at low RPMs (like going up an incline in a high gear). The car used to 'grunt' (low frequency growl) in the same situations before, so I think it's resonation coming from the manifold being amplified by the intake.
Now I'm waiting for the tune and will drive it for a few thousand miles before I decide if I can live with the noise or not. Cruising on the highway it doesn't happen much.
Funny we had the same engine light experience. After a day+ the light went away. Cold start this morning (same temps as prior morning) very little rough idling. I think the engine is slowly adapting to the intake. Can't say I notice much improvement, perhaps a bit when really pushing it hard. It does seem even more responsive than before, which is saying a lot because the tune alone provided a lot more response over stock.