CompareTo only compares the Width*Height of both images. This is what you are looking for:
using (MagickImage navy = new MagickImage("xc:navy")) { using (MagickImage blue = new MagickImage("xc:blue")) { double distance = navy.Compare(blue, Metric.RootMeanSquaredError); Console.WriteLine((Quantum.Max * distance).ToString()); Console.WriteLine(distance.ToString()); } }