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.
Sorry to hear that. I just tried to slice the parts again in the slicers I have installed: KISSlicer, Netfabb Studio Basic and cura (modified skeinforge). cura flashed a few errors for the core but sliced it without issue. All slicers showed no problems in the gcode visualisation at all. Netfabb usually screams at you as soon as you load the model if there's an issue, it didn't for these.
You're also the first to report a problem of the 200+ people that have downloaded the files so maybe something got corrupted in the download? Or maybe it's slic3r that is having some issues? I do remember hearing some people have a few issues with that slicer on some models.