Sometimes .savs are encoded in different format from flashcart to flascart and this applies just as well on emulators. Try converting them and naming them properly according to the ROM you're using:Game works on DSTwo, clean mode. However, my save from the Japanese translation version 1.5 didn' carry over for whatever reason. Any reason why? USually I was able to rename it!
http://shunyweb.info/convert.php