I have a perfectly flat object (lofted it myself out of a 2d shape, it is 100% flat!)
S3D somehow creates several additional layers on the top and bottom (sides) of the print.
You can also see that phenomenon on the failed brim which only covers a part of the prints.
Just slice the model and watch from side, you can see 3 layers there that should not be there on top.
Then watch it in layer #1 view after slicing and you can see the brim is attached to these "abnormalities" and the remainder of the object floats in air.
Caused a huge mess in my printer when I didn't notice it, no bed adhesion.
Why does S3D add additional layers on top and bottom of the print ?