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MakerBot Print is our newest print-prepration software, which supports native CAD files and STL assemblies,
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It must be something specific to Cura. I loaded up Cura and tested and have the same issue.

I used Slic3r to slice and generate the gcode for these prints and there were no issues.

When I get a chance, I'll try to rebuild the model from scratch and see if I can generate a model that will slice cleanly with Cura.