I'm stretching the limits of the slicer with bad model behavior... and expecting it to behave just how I expect it would, which isn't terribly fair.
I often design objects comprised of cubes on a 3D grid. When 2 cubes on the same horizontal plane have touching corner edges but nothing else, this results in a non-manifold .STL. S3D does a remarkably good job of slicing these (especially if you move the object around on the build plate a little when slicing errors are encountered), but it doesn't properly calculate open spaces when this happens. I get it... and honestly I'd rather trim strings than shred filament from too many retracts.
I created a bunch of test shapes, all of which sliced correctly without a non-manifold edge involved.
I've attached a screen grab with the problem area highlighted. You can see that there are no retracts on that non-island. If only I could have my cake and eat it too...