Yep. This is it. There was a guy on here who did a polarity test and found that the sensor would only react to negative polarity magnets (I think). So that's why we're seeing that some iPad 2 cases work and others don't. The location of the magnet didn't change at all.
And I'm that guy! Although, I'm not sure which pole (positive or negative) the iPad 3 is expecting.
Apple switched to using a sleep/wake sensor that is sensitive to the polarity of the magnet. The iPad 2's sleep/wake sensor didn't require a specific polarity, it worked with both ends of a magnet. Not true for the iPad 3.
Everything is detailed in a post on my blog (complete with HD video demonstration):
http://markshangout.com/blog/2012/3/17/ipad-3-smart-cover-sleepwake-feature-not-working.html
Mark