Really?
That sucks.
Here's the thing, I recently transferred all of the save files from my Memory Card 251 onto a 64Mb Nyko Memory Card. While I haven't tested all of the save files for all of my games - the ones I have played since copying the files load the duplicated save files without any problems.
Could it be some sort of electronic serial number that ties the save file(s) to a specific machine. A digital security system that tells the GameCube that the Memory Card data was created on that machine or a foriegn (meaning not yours) GameCube, where it would be readable but "copy protected" as a deterrent to "cheating"?