Hm...I have never used an M3 DS Real, but I'd think if there is an option for save types, make it correct. If not, make sure you have the latest firmware and that your flash card or whatever you are using isn't bricked or corrupt. Sometimes you will need a donor card as well. That may be your problem. A donor card is a retail ds game cartridge that could save your rom's saves onto it. Of course, only some certain cartridges work. Luminous Arc can be used as a Donor I believe. Because RPG's have a better save system than most games. You would insert the card right before you start the game, in the game list menu. If that's not the case, then its just the format as the error says. Sometimes errors mean many things, but can be simple too.
Anyways, make sure you have patched the new rom correctly, and that it is compatible with your card. Also the rom might just be junk.
Good luck.