Some of the cheaper cards (and USB keys back in the day) sort of assume you'll use a single FAT[/32] partition and they understand the FAT and use it as poor man's TRIM information. They get super upset if you attempt anything that is not a single FAT[/32] partition. Some will actively forbid it by ignoring writes to the first sector of the disk and of the partition. Perhaps this is one of those cases?

EDIT: technically this is kosher as SD spec mandates FAT32 (just like SDXC spec mandates exFAT)