MakerBot Print is our newest print-prepration software, which supports native CAD files and STL assemblies,
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I presume you used the Euro version, so you probably downloaded this file? https://www.thingiverse.com/download:5577105

Which Slic3r version are you using? I'm on 1.3.0, and it sliced the basebox mesh with no problems (see attachment).

To check whether it's a slicing problem or a graphics problem, you could try to switch to the "Layers" view and check the bottom layer (see 2nd attachment). Just to make sure the preview is really correct ...