Many new Apple iPad 3rd generation owners have been reporting problems with their third-party smart covers (the one’s that aren’t made by Apple), the one’s which was originally  made for the iPad 2.  From this video below you can see:
The official smart covers (by Apple) also didn’t work well with the new iPad, but Apple in a very short period of time, replaced the magnets with new ones that are compatible. This big problem that the owners face is, that the third-party smart covers don’t lock their iPad 3.
This issue is getting more known day by day and all the accessories companies will be aware of it, and change the polarity of the magnet soon, so don’t worry.