Ok, if I set First layer height into 100% and set the First layer width to 100%. The S3D wants to fill up the bottom of the part even that is not in 3D-model. And what is "fun" about it, is that it makes the solid bottom into air. It is 3rd layer (yes I tried to print it). If I change the first layer height into 95% or 105% it prints just fine (removes the solid bottom). So this is not major issue, but it did some WTF moments to me.
Here's some images from S3D to show what I mean: