Hmmm...it seems to me that your game save (or saves) is corrupted, if hot the Rom itself. I don't think the problem's your card.
That happened to me with one of my games once before. What I had to do was delete the ROM itself, then delete all the files associated with the ROM (.sav, .is0/1/2, .opt, .bkm), then download a new, clean ROM, then change the ROM's number (in my case, it was from 0731 to 0732). When I loaded the game, it created new, clean save files and loaded fine as it did before.
Of course, this will result in lost save data.