perhaps you used the incorrect savetype?
Sorry but it's been ages since I tested NeonDS but even then I don't remember this occuring to me so I am afraid I can't really help and very few people use this emu due to lack of sound and various problems it has with other games so it's unlikely you will get much more feedback than this. Just about everyone uses DeSmuME or no$gba these days with a couple of people using iDeaS.
Sorry but it's been ages since I tested NeonDS but even then I don't remember this occuring to me so I am afraid I can't really help and very few people use this emu due to lack of sound and various problems it has with other games so it's unlikely you will get much more feedback than this. Just about everyone uses DeSmuME or no$gba these days with a couple of people using iDeaS.