This image is a 0.25 first layer. The scar on it suggests over-extrusion or under-retraction. I've tried reducing the the extrusion multiplier (down to 90%) and it doesn't seem to change anything at all, it always looks like this:

Using a Prusa i3 from Prusa himself (not some random kit). I have this problem in general, not just with S3D.
S3D settings
Process: http://shop.prusa3d.com/forum/download/file.php?id=533
Factory: https://dl.dropboxusercontent.com/u/331 ... ds.factory