It seems you have to reset the 'page' of the image before you do the next crop. You can find some information about that here: http://www.imagemagick.org/Usage/crop/#crop_repage. Your code would become this:
_magickImage.Crop(new MagickGeometry(1340, 47, 924, 1144)); _magickImage.RePage(); _magickImage.Crop(new MagickGeometry(0, 0, 100, 100));