Well, figures look a lot better changing the last command to saveas:
% imwrite(X.cdata, [C{1}, '_', inputname(2), '_vs_', inputname(1),'.png'])
saveas(gcf, [C{1}, '_', inputname(2), '_vs_', inputname(1),'.png'])
I'm still interested in improving the appearance of my figures, so any advice is welcome...