Quick update, could it be Cura?
The 2 prints I did was using Cura Wanhao edition and then the latest version.
Last night I did the same print object but I used Repetier host and used slicer as the slice engine. I tried keeping the settings the same where I could.
Other than calibration issues I.e. the Y on the cube looked a bit off near the top, the cube printed with no issues