The issue has to do with S3D's thin wall behavior, which is a major topic of discussion on this forum. S3D will only fill with perimeters in a solid fashion if the wall thickness is approximately an even integer multiple of the extrusion width. It can be slightly less than that depending on the amount of acceptible perimeter overlap you have specified.
If it is not an even multiple, S3D will either fill it with your standard infill pattern. If the the gap is less than a single extrusion width, S3D will often leave the space between the perimeters empty.
A number of us are begging for the next version to have improved thin-wall and gap-fill behavior in the next version. You can read about it here: viewtopic.php?f=23&t=3471