The fact you are using nintendont means you have the Homebrew installed. One cool feature using nintendont is you can store the save files on the SD Card. A useful feature if you don't want to flap around with memory cards / don't use a GameCube. Plus you don't have to worry about corruption.
But yeah, some games are programmed so you can't copy the save files. Soul Calibur II and Super Smash Bros. Melee come to mind. Some like F-ZERO GX and Phantasy Star Online will only work if the Serial Number of the memory card is the same.
There is this really cool Wii app called GCMM (http://wiibrew.org/wiki/GCMM) which can backup save files, even the ones that have the save copy protection. Using 1.3V or higher, it can patch F-ZERO GX or Phantasy Star Online to work on any memory card.
Also, if your Memory Card becomes corrupted and asks you to format the card, DON'T. It's most likely the header that has corruputed, and the save files are perfectly fine. Just back up the saves separately (not as a raw), then format the Memory Card in the GameCube or Wii's settings, and then restore your save files.