Even though this happened a long time ago, I have some questions if you could answer them. When you were saving in both versions, were you "saving a lot of data" Infamously in Gen IV, when you complete an important event or literally just mess with your PC boxes, the save box will say "saving a lot of data" and take longer than usual. If you could load both of your copies, do the exact same thing in both copies, and tell me if the time still differs, I might be able to figure this out.