This has nothing to do with turning on Spotpass. Does Luma say "Booted from CTRNAND via B9S" when you hold Select on startup? Because that means your 3DS is not reading your SD card for some reason.
For starters, you can try taking your SD card out and putting it back in again. If that doesn't solve the problem, you'll need to check your SD card more thoroughly, as they fail with alarming frequency: connect your SD card to your PC, copy everything off (preferably with
Roadkil's Unstoppable Copier), format the card, test the card with h2testw, and copy everything back again.