I had this problem and I found a way to solve it. So what I initially did was opening up a nds file for Diamond on a file named Pokemon Diamond. However, the problem was when I tried to open up a ds save file on another folder, there was the same title. "Save File shorter than SRAM." So what I did was, I copied the ds save file and put it into another folder, called Pokemon Diamond DSI save. I also copied the nds file for Pokemon Diamond and put it into the Pokemon Diamond DSI save. This should help you.
