I get a knocking sound occassionally, not with autostop, but usually when I first start my car and am in reverse. I'll get the knocking sound as I brake before switching into drive. I asked about this at the dealership once and they say it is a common thing on certain Honda models. I forget the technicalities of it but it boils down to there being extra space between some parts (helpful aren't I? LOL) and that causes the knocking sound. They gave me a paper diagraming the issue, but they have no solution for it other than to insert a business card thickness piece of paper to prevent the gap. Boils down to just a quirk and nothing to be alarmed about.

sarah