MakerBot Print is our newest print-prepration software, which supports native CAD files and STL assemblies,
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I never used s3d slicer with this design... did you try it with cura or slic3r just to see if you see same kind of defect in preview?... honestly I've printed multiple of them using both of those slicer without any issue... ( more than 10 )...
I seems to be related to the slicer but you could try some mesh fixing utility to see if this fix your issue... (s3d have some/ meshmixer/etc.)