You’ve got the mystery GH blues, brah. So sorry for you.
What about applying contours to a surface instead of the mesh? Oh, I see the problem with that; your current mesh effectively has two surfaces, top and bottom… 
And by the way, I’m not going back to SDiff, it’s way too slow with no advantage.
P.S. For whatever it’s worth, here is an adaptation of the model from the other thread that gets the top and bottom surfaces separately. As you can see, the edges cause GIGO artifacts.
surface_from_points_Ryan_2019Nov24a.gh (922.5 KB)
Is it possible to get the top and bottom meshes separately? You could convert them to surfaces before adding the vertical edge surface that connects them, to create a “Closed Brep”. Perhaps then get cleaner results from Contour?