I got my answer - Nintendo actually has a support phone line, who knew?
Apparently 64GB is TOO big and they don't recommend that size for 3DS - they recommend nothing over 32GB which I think is BS, but hopefully I'll never need all of the 32GB since they all come with 4GB and I haven't needed to expand until this point.
Anyway, got a 32GB card, formatted and copied the same way, issue resolved!