Its simply the way the N-Card is saving:
Ill append (Orig) and (New) and try to keep it simple =$
// Usual way of saving
You play [GAME] , [GAME].sav is written in a temporary place.
You turn off your DS, the savefile is still at the temporary place.
You turn on your DS and go to the Game-Selection-Menu, NOW [GAME].sav is written to the card.
// So what you do is:
You play [GAME] , [GAME].sav(orig) is written in a temporary place.
You turn off your DS, the savefile is still at the temporary place.
You hook up the card with your pc and copy the (new) savefile to you card.
Now, when you start into the Game-Selection-Menu, the [GAME].sav(Orig) is 'copied' from the Temporary place to the game, so it overwrites your [GAME].sav(new)
--
Simple way around it:
Before copiying [GAME].sav(new) to the card, play [ANY-OTHER-GAME].nds.