We need a little bit more info. If you're going from a previous version of AKAIO, you might have set your previous game saves to save as *.nds.sav files. That was the default since 1.4 (I think) and it's the default for the official firmware from AceKard. The current extension is *.sav and there are a few batch converters in Filetemp. You can also change the game saves on a case by case basis. You just need to have AKAIO display all files (I'm not sure you can see *.nds.sav files with the .sav option) and then view the file's properties if I recall correctly. There could be an option there.
If you're using another card or a PC emulator, there are other steps.
Gamefaqs has a faq that mentions they only accept save files in Gameshark or Action Replay format to help cut down piracy, but there is an online converter that will change them to RAW format. Google "shunyweb" for the site.