Well, there seems to be no set pattern.
It's just some cards work, some don't.
I went through the exact same procedure with each card in this list.
MiniAide Fat32 Formatter Home Edition 1.05 and deleted all partitions then add a single FAT32 partition
DiskWriter 1.6 and re-Formatted twice, then Formatted twice, then used Sonic's template0312.txt and wrote OoT into two positions with verify on.
Added Sonic's US Save to both positions.
Booted the 3DS with the Sky in it, "Blue Buttoned" twice then launched OoT
Opened the GATEWAY***** save and it took me to the hut.
Then.....
In the SKY3DS:
Toshiba_ 4GB_ Class 4 - Works
Kingston 4GB_ Class 4 - WSoD
SanDisk_ 16GB Class 8 - WSoD
SanDisk_ 16GB Class 8 - WSoD
SanDisk_ 16GB Class 8 - WSoD
Kingston 16GB Class 10- WSoD
SanDisk_ 32GB Class 4 - WSoD