So I think my program is just fine. I think it's my SD that's messed up. Someone else tried my game and the saving was working just fine.
I think that maybe gmenu2x messed things up, or at least was affected by the same problem. When I create links in there it, it ends up writing out 0 byte files, just like my app is. When I try to delete these from windows, the files are locked and I can't delete them. This all happened before I added saving to my app and after I installed gmenu2x. Maybe it's just a coincidence, but a format is in order I believe.