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 normally see problems from non manifold models in the slicer, but that could be an artifact of my tool chain. Slic3r makes the tool path visible, and when a manifold issue breaks the print, it will normally wipe out many layers.
Anyway, the model is fixed, hopefully that solves it. If it doesn't, let me know and I'll dig deeper into it.