It might be running in a lower color mode when you run it in progressive scan. There are a few Gamecube titles that had no transparency dithering even on S-Video (trust me, it shows up on S-Video if it's there), but did in 480p. Eternal Darkness was one of them. The same thing's been observed in Wind Waker and Excite Truck. Also, the Cube used a deflicker filter of some sort in 480i mode that was often the only antialiasing games had, thus introducing aliasing at 480p.
OTOH, some people say RE4 didn't dither in 480p, although it was obviously running in 6:6:6:6 color mode and had pretty significant banding and aliasing. And then there are games running in the high-color mode with plenty of tranparencies and no dithering, like F-Zero and Metroid Prime. So there are ways around it, but obviously, it's a bit of a trick.
OTOH, some people say RE4 didn't dither in 480p, although it was obviously running in 6:6:6:6 color mode and had pretty significant banding and aliasing. And then there are games running in the high-color mode with plenty of tranparencies and no dithering, like F-Zero and Metroid Prime. So there are ways around it, but obviously, it's a bit of a trick.
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