As long as your SD card is inserted, this error shouldn't happen.
Are you sure the first partition of your SD card is formatted using FAT32 (I don't think any other format works on the 3ds, but still)?
Try running Decrypt9, does it mount your SD correctly?
Otherwise, try running Cakes 85. That's a release before I added Normatt's new sdmmc.c. Maybe that's the problem?
First partition? I only have one partition on my SD-Card...or am i missing something?