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.
Look at running your meshes through netfabb, seemed to fix it for me in S3D. Prusaslicer has it built in, witch is probably why it works there. https://service.netfabb.com/service.php