Topic: 3DS and SanDisk Ultra SD card compatibility?

I recently got a 32 GB SanDisk Ultra SDHC card, copied the folders as-is from a 4GB SD card to it on a PC, but when I replaced the card into my 3DS, it had trouble recognising the card. 3DSware apps kept appearing and disappearing from the screen, sometimes they would launch while most of the time it would either say the 3DS card was removed (it was not and had never been removed while the system was on) or that an error has occurred and the system would now restart. The 3DS would play music and show photos from the card, but most 3DSware games would exit with error and eShop would give an error mid-download saying there's no card (after which it refuses to display the store.)

The 3DS still reads from the 4GB card without problem and the folders are backed up so there's no data loss, I'm just not sure what to do about the card now. So far I've tried:

• Checked that the card isn't locked
• Re-formatted the card (FAT32) using both the computer's formatting and the SD card formatter from sdcard.org
• At first I thought the card was corrupted so I took it back to the store and exchanged for another one, and the same happened, so unless I'm having a distinctly unlucky day, the 2nd card at least should be functional?
• Starting with the card formatted blank and re-downloading the 3DSware (eShop works but the games would give the same error)

My question is, has anyone used this card with their 3DS, are these glaring symptoms that the card isn't compatible with the 3DS or is there another cause?

Thanks in advance!