I was so busy checking out the new iOS 4 features like folders and wallpapers, it took me a while to realize that the icons that used to be transparent now draw a black rounded-corners square behind the icon.
This is most certainly because the new wallpapers implementation draws shadows and glows around the icons to increase the readability and make the icons “pop out” independently of the image you set as your background.
So watch out while designing your next app icon!