Yeh, it's a common error which has happened to me on few roms, I always just boot Ysmenu.nds delete the dodgy save file and then fire up the rom with Ysmenu, the save gets created properly then.
note, that if you use cheats, the .arp file will suffer the same fate, so just use the y's menu if you wanna cheat in these cases. or rename the .arp file too as explained in the post above this.