After the over heat issue now it the new iPad 3 is having Smart Cover incompatibility issue. Those new iPad 3 users who had flipped their old Smart Covers from the iPad 2 are complaining about the new iPad not functioning well with it.
The issue is due to the new iPad 3 having polarity specific sleep/wake sensor which the iPad 2 never had. For the Smart Cover to work perfect with the new iPad it has be functioning under a certain range of specific polarity and hence it can cause compatibility issue. Wile many new iPad users have complained about it some users are reporting it be working completely fine.
However if you do experience this error the only solution for this would be to get yourself a brand new Smart Cover for your new iPad. The new Smart Covers cost about $ 40 and are confirmed to function properly with the new iPad. You can buy on from the Apple Store right away.