It appears that the sleep/wake sensor in the new iPad is sensitive to polarity. Apparently, with the iPad 2, some customers were having issues with their iPads going to sleep when flipping the smart cover to the back of the device. By changing to a sensor that is sensitive to polarity this problem can be eliminated.
According to the site, sometime in 2011 Apple changed the design specifications of the Smart Cover in preparation for the release of the iPad 3. The newer Smart Covers have a different model number.
Apple is apparently willing to swap out an old Smart Cover for a new one if you are suffering from the issue.