I think I figured out why the result from the command line is different then from Magick.NET. Magick.NET uses HDRI (http://www.imagemagick.org/script/high-dynamic-range.php) and it looks like there might be a bug in setting the channel depth in ImageMagick when HDRI is enabled. I will let get back to you when I know a bit more. Setting the bit depth to 16 bits did solve the problem for me.
p.s. The order of your matrix should be 3 instead of 4.
p.s. The order of your matrix should be 3 instead of 4.