There's an article floating round somewhere about random compatibility problems between old smart covers and new iPads. If I remember right, this is how it goes.
The first iPad and Smart Cover magnets and sensors were not polarity sensitive. This occasionally cause problems when you flipped some third party covers all the way around to the back of iPad. To get around this Apple has apparently made the new iPad's sensor polarity sensitive. It matters which way the magnet is oriented in the cover.
Because it did not matter with the iPad 2, there was probably no process in the manufacturing of Smart Coves to place the magnet one way or the other. So some covers have the magnets polarity one way, and others the other. That makes for unpredictable behavior of an older cover with a new iPad.
Supposedly the newer covers (since they changed the model number and little else) are constructed with a standard polarity.