For those that have the "3DSCARDNAND" instead of "R4ICARDNAND" SDcard: In order to let the Emunand Tool 1.0 recognise the SD, you have to...
1) Dump the entire SD content with Win32 Disk imager
2) Download an hex editor ( I suggest the freeware HxD from here:
http://mh-nexus.de/en/downloads.php )
3) Hex edit the SD card dump and change on the first line "3DSCARDNAND" in "R4ICARDNAND". Save the file and exit from HxD.
4) Using Win32 disk imager, restore the modified SD image into the SD card.
5) Open emuNAND tool 1.0: it will recognise the emuNAND SD
Tested and working method.
I hope this can help someone
I also used the dump generated to restore the 3DS from Gateway-brick.