Hi Churlzu,
A lot changed from R2014a to R2014b (and on onward), primarily in terms of the graphics. A list of the major changes can be found here: https://in.mathworks.com/help/matlab/graphics-changes-in-r2014b.html
To the specific queries that you raised:
- Change of Color
The change of color is an expected result due to the change in the way graphics is handled. This has been captured in detail in this link: https://in.mathworks.com/help/matlab/graphics_transition/why-are-plot-lines-different-colors.html
- Issue in Transparency
I think this MATLAB answer addresses the issue from the backdrop of changes in Graphics from R2014a to R2014b: https://in.mathworks.com/matlabcentral/answers/168264-how-do-i-set-transparency-of-area-plot-in-r2014b
Abel