There have been a considerable number of complaints about some genuine Smart Covers not fully working with the new iPad. This, it turns out, could boil down to there being two different types of Smart Covers, which feature different magnets, MacGeneration reports.
Apple changed their Smart Covers in October 2011, modifying some colors, but more importantly changing the hinge so that it no longer scratched the iPad and the magnets inside. This might be the reason why in some cases, but, according to MacGeneration, some Smart Covers bought brand new today are still not fully functional in terms of putting the iPad to sleep and waking it.
Another possible reason is simply that they were manufactured incorrectly, and this would explain why the problem exists in both generations of Smart Cover. If your Smart Cover does not fully work with the new iPad, I’m sure that as long as you provide proof of purchase, Apple won’t mind exchanging it.
The magnet layout and cover compatibility is still a bit of a mystery with the new iPad, so we’ll have to see if Apple come up with a Smart Cover update specifically for their new device.