Thanks for providing the .factory file.
I fired up my copy of v4 and the model sliced as you'd expect.
Moving onto v5.0.1, first thing that I'd noticed is that your model isn't manifold (a completely solid model). This is what's leading to your
issues with the missing layers at the bottom of the print (the red line on the image below indicates where the non-manifold
break is... and this applies to both sides of the model).
In order to get v5.0.1 to "correctly" slice the model as you'd expect, you need to go to the
'Advanced' tab in your process and
change the model slicing/repair behaviour. I've indicated the settings that need to be changed in order to achieve what you're
looking for.
Ultimately to correct the model, you'll have to go back to Fusion360 and combine all of the bodies in your model to make it a
valid solid (manifold), export the STL then slice it again in v5.0.1.
Hope this helps,
D.
You don't know what you don't know until you know (my philosophy for continued learning).