I had just this experience with our new iPad 3s and two Maroo leather folio cases. One of the Maroo cases worked perfectly (on both iPads) while the other wouldn't active the auto sleep/wake when the cover was closed/open.
A little detective work with a magnet revealed the reason for the problem. I've posted the story and an HD video demonstration to my blog:
iPad 3 Smart Cover Sleep/Wake Feature Not Working