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. Just finished printing bottom one. The trick was to open the original STL in Blender, and subdivide it once.
Either the STL has some issues (I didn't try to export without any change to test this), or Cura has a bug. I have Cura 15.04 and Printrbot.
Thanks i3D for great model.