The World Ends With You: Saving Problem

I've played this game for a solid 3-4 hours and had saved throughout my play time, but when I went back to play there was no save file, so I checked the file on my computer and it was .nds.sav so i thought it should work properly but is not, if anyone could help me, that would be great :)

More info then,
http://forum.romulation.net/index.php?topic=1736.0

I am having the same problem with my rom except I'm using R4i latest firmware can anyone help?