I am happy to say that this issue with inner perimeters missing has now been fixed in Version 4.1.1. Our team successful tested your factory file in the latest version and the inner perimeters were showing in the preview.
You can download the latest version by logging into your account on the Simplify3D website and proceeding to the Downloads page. There were many other fixes and improvements in this version, so you can view the other changes at the link below:
https://www.simplify3d.com/software/release-notes/
Thank you for posting your screenshots in this thread and for bringing the issue to our attention!