I have the same problem for my old 1gb micro SD. But I fix it as below steps.
1. Format it to ext3. (Use special software or Unix/Linux machine to format through card reader)
2. Put it in the kobo and connect it to the computer.
3. Win7 asked to format the SD card. Then format it to fat32. Copy books in the SD.
4. Disconnet kobo and I found the books in the library.
Hope it can help. Good luck!
And I suggest kobo to add the format card function in next firmware.
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