MakerBot Print is our newest print-prepration software, which supports native CAD files and STL assemblies,
allows you to interact with all your printers via the Cloud, and many other exciting new features.
I had the same problem. I used the Repair menu in S3D and selected "Remove duplicate triangles" once and then "Remove orphaned triangles" once. That fixed it for me and it prints well. (Note you can keep removing orphaned triangles and it turns into a mess. Don't do that.)