The above post is correct, it's formating/preparing/whatevering the save. Just wait a while.
If after, let's say, a few minutes the message doesn't go away, try to defragment your SD-Card. I once couldn't load my saves in FF3, and once I defragmented my card it worked again.
If THAT doesn't work, try to put the ORIGNAL patched rom on the card, start the game, save once, and transfer the save to the patched version.