CURA - Adding Layer over Opening - Bug

Okay guys I am seeing some weird results with Cura (20.01 and latest).

I have a model I have sliced apart, and added holes in for alignment pins. In EVERY editor, including CURA I see this opening honored. However, when I switch to g-code viewer, the first layer, shows a layer of filament, covering over this whole. Here are photos of what I am talking about.

What the heck is going on? I know the models are considered “damaged” as I sliced them up with Netfabb and reassembled in Blender

(Notice the model is flipped)