I have this exact same issue with Super Mario Sunshine if I enable the 60FPS Gecko code found on the Wiki page. For some reason, this does not happen with the 16:9 code. I have yet to try any other cheats.
EDIT: I realized I was using an AR code for Widescreen, which may be why it's working.
EDIT: I realized I was using an AR code for Widescreen, which may be why it's working.
