New thread as requested.
Issue: Slicer is filing in holes that should be there. The presliced image looks fine and other slicers like Afinia/UP! and MatterControl don't have a problem with it.
May I advise that you can very easily separate intersecting/overlapping within S3D by using the Separate Connected Surfaces option. This somewhat mis-named option will separate the meshes out into separate "models" .....and S3D will then combine them for the purposes of slicing.So, the STL file has to consist of one single object? Hadn't run into that requirement before, guess that's why I've been having trouble with S3D. The other slicers I use for our other printers (we have 3 currently as we sell a lot of 3D printed stuff) don't care how many objects there are and handle the merge/overlap just fine.