You have to set FaceColor to 'flat' in order for CData to take effect, which you are doing for the first bar but not for the second.
figure('Color','w', 'Units','normalized', 'Position',[0.3906 0.6778 0.2037 0.2514])
yDataGreen = [ 5 7 9];
yDataRed = [ 6 8 10];
xData = 1:3;
barPlot1 = bar(xData, [yDataGreen; yDataRed]) ; hold on; grid minor; box on; title('Now that does look like the Red you want')
barPlot1(1).FaceColor = 'flat';
barPlot1(2).FaceColor = 'flat'; % set both
% or set both at once:
% set(barPlot1,'FaceColor','flat')
barPlot1(1).CData(:,:) = [0 1 0; 0 1 0; 0 1 0]; %green
barPlot1(2).CData(:,:) = [1 0 0; 1 0 0; 1 0 0]; %red
