Some of the icon names probably changed from the iPad 2 versions due to the resolution change. For example, where an app/theme may have used "Icon60x60@2x.png" as the main icon for the non-retina version, they may now use something like "Icon72x72@2x.png" for the retina version. Those are just example names, but you get the point. I've found this to be the case when manually changing icons on my Retina Mini.