The problem could possibly be the memory card.
I've had the same issue a few times with another game, and after searching google for a solution I found many people saying that this is sometimes a problem with third-party memory cards. This coincides with what happened to me because the card which I have problems with happens to be a third-party card, while my cards manufactured by Nintendo have never had this problem.
Also, there are threads about memory card corruption on
techforums.nintendo.comYou may be able to find a helpful solution there if not here. Good luck, and I greatly hope that you are able to resolve the problem.
3nodding 
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