That's a pretty bad glitch, not as bad as mine, sometimes when I enter a room, the TV goes black, comes back, and then I can't move or anything...
ANYWHO, I hope you get a new one or it is fixed....somehow.
I think MM is one of the best even though the replay value is not really something I like to do in the game. It is hard.. but lots of newer Zelda games lack challange to me.. in my opinion.. Also.. like others said.. if you are saveing then there should not be a problem.
Is there something wrong with your memory card? =O