1st, I alway recommend just one wiistation at a time in the app folder, there can be some weird things if there are too many apps in this folder. For renaming, alway do it from the pc then put the file back on the sd, I knows it weird but I've seen some bugs about that. if you don't understand the question, sorry I can't help much more as I always ask question that cannot really be clearer, also you've talk about two games at the beginning, now it's 4 games.
@xjsxjs197 has made changed changes to the memory card code, so that means that your old saves on the sd could be not operationnal with the latest version, pretty obvious that in that case, you must erase saves with this version and restart from the beginning of the game.