Layer height issues creating partial top layer
Your model isn't perfect. I took it into Windows 10 3D Builder for simplicity. I kept clicking the "Mirror" function and noticed as it basically flipped there is some slight movement. I measured some points from bottom to top and noticed some differences. 

Try to take your model into some software to fix/flatten it. Or recreate it making sure its perfectly flat on both sides. It is definitely not your Cura software.