MakerBot Print is our newest print-prepration software, which supports native CAD files and STL assemblies,
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I've found one problem, when slicing the parts the bottom magnet holes on the cups disappear. That of course explains my aforementioned irritation, sorry for that. I've sliced with cura. Before slicing cura shows the holes correctly.
I used 0,2 layer height and 5% infill as per your isntructions. As for shell options I left everything standard. I attached screenshots for you to visualize the problem. Also here in the comments I found someone who had the same problem?