From those screenshots, it seems like iOS 5.1 is using the traditional auto-resizing properties of the views, whereas iOS 6 has been explicitly programmed to use an alternative layout, in a similar way to how developers create separate interfaces for iPhone and iPad.
Put plainer, the iOS 6 Springboard has been specially coded for this precise resolution, and this resolution alone. This is very convincing evidence for a taller next-generation iPhone.