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 know it's been a few months since this comment...but if you're still looking at trying to fix things, I'm using Slic3r PE. I have all of the white/black done, and I'm starting on the grey. Everything has printed fine so far.