I have a similar problem in Pokemon mystery dungeon explorers of sky. Before i helped the shaymin(late in the game/post-game), it saved without crashes but after that i cant save anymore. If i save and reset the Emulator it crashes and my save file is gone.
edit:
i tried to reproduce it but now...
@Xdqwerty good. thats great fma takes more time to to build up the beginning. brotherhood rushed the beginnign because the beginning had already been told