MakerBot Print is our newest print-prepration software, which supports native CAD files and STL assemblies,
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Weird indeed! Do you use the "xy correction" setting? That's one setting that might affect thin structures. (There could be others I'm not aware of.)
I guess I'll upload another version with thicker mesh,as even if we find the correct Slic3r setting, another user had the same issue with Cura, which I don't know so well.