Last Update: I now 100% know the issue: The less I pressed reset, the less the save data actually saved. That also means pressing it too little can corrupt the save, it also explains why I didn't have the issue in Mario Star Road. Mario Star Road only has 4 or 5 conditions it saves (stars, coin high scores, unlocked doors, switches pressed) which is very little. I recommend you pressing it 25 seconds or more every time you save in a big game like oot or donkey kong 64, in tinier games you can just do 10 seconds and it would work perfectly fine. In Star road you can even just do 3 seconds or less