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 am working on a fix to resolve this issue. In the mean time, if you're using Cura, turn off Print thin Walls, turn on Fill gaps between Walls to 'Everywhere'. This prints fine with my S3D profile.