MakerBot Print is our newest print-prepration software, which supports native CAD files and STL assemblies,
allows you to interact with all your printers via the Cloud, and many other exciting new features.
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 ...