Aw man, my friend said the save failed when loaded by a retail XD game. wtf. I'm going to do some more testing...
Edit: Once I get my memory card back that is...
Edit 2: Using the same base memory card file I started a new XD game on both cards. I'm looking at them in a hex editor and they have some differences... I haven't even started the main story either so it's all the save protection.
I wouldn't have to do this if the damn app didn't corrupt the memory card. :/
Edit 3: Wow, the only difference between the two seems to be at the two addresses 0x2A and 0x2B. Except when I change one save to match the other it says the Memory Card is corrupted instead even though the CRC Checksum of both save files is the same (as in they both contain the EXACT same data). WTF.