I really think it's in how carefully the pieces are assembled. It seems that the magnet on the second one is in exactly the wrong place; if I FORCE the cover to be square, instead of where it wants to be naturally, there's no problem. If it slides just a little bit out of square, the Kindle goes to sleep... sorta. It's not always a "clean" shutdown.
I think they may have just received a fresh shipment from the factory. The first one didn't really have any smell that I noticed, but the second one has a smell that I can smell on my hands, even with the cold that I'm fighting. It's not a plastic/resin smell, it almost seems like a leather smell, although I doubt there's any leather involved.