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.
Still not quite sure what the issue is... however I checked all the .stl's and there are no issues according to my mesh checker. These have been printed by thousands of people and the vast majority get a great result...
Having said that, if anyone has an issue with this type of thing, they all too often use Slic3r. It is a slicing app problem as it doesn't seem to deal with the complexity of some designs as well as other apps. Cura seems better and I never have issues with my MakerBot Print.