So you don't have any .sav file on your microSD card that gets updated? I don't like the sound of that (in case of like hardware failure or anything, I like to have backups.)
Edit: I should clarify, when I rename Mother3.sav from ExpLoader to Mother3.gba.sav for AKAIO, and then load the game, in the game it tells me "Data Corrupt. Save file(s) deleted."
And when I do the "Dump SRAM" from the 3-in-1 menu, it gives me a 512kb file for a GBA save. The save from ExpLoader is 64kb. But if I load the old save in Exploader 0.58b, and then go into the game from AKAIO, it only gives me the option to create a new game, and not load game.
Edit2: I turned on the save/load prompts for GBA, cleared out the NOR, and then re-loaded Mother 3 to it, and attempted to start a new game, and saved that, and even still, after saving it on a reboot, and then loading the game again, still it only gave me the option to start a new game. I wonder if this is a Mother 3 related problem, or a NOR related problem? Anyone know any other 32MB games so that I can test it?