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.
Use 3D Builder (comes built into Windows 10) it does automatic model repair, and you can export to STL if your printer is not already supported for direct Ctrl-P printing. As to why this manifold issue happens: it's a common problem with models produced by composition in OpenSCAD and similar tools. I haven't found a sure way to avoid it all cases.