I update to Cura 3.0.3. I was using the Wanhao edition of Cura previously. Worked fine for me, thought to jump to the newest yesterday. When I read the FAQ, I understood that 3.0.3 would migrate settings if installed side by side to the old version.
Here is screenshot of some gears I am trying to print. 3.0.3 is infilling the bore. This is under both recommended and custom settings.
In 3.0.3 the Mesh Fixes -> "Remove all holes setting is unchecked.
I used the same .stl that I generated from AutoCAD for all 3 gcode generations. I put it into S3D too to check the model.