I've also been having trouble with Golden Sun. Worked fine for the first couple hours but then started giving me problems. Getting close to a wall in some dungeons causes a small section of the wall near me to disappear. I've now hit a spot where it crashes every time and cannot go any further (ice dungeon after getting the Mia character, during the small scene immediately after the Djinn battle).
I downloaded a new rom file but that didnt seem to help either. Any suggestions?