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 just confirmed that the file that is uploaded has no holes in it.
Some things to try:
I suspect the Slicer is having a problem with something in the model. I have ran into some strange issues with slicers when the models are a little complex and detailed. Often the issues get resolved with the next release of the slicer. But it is a good thing to bring this issue to the people who created the slicer so they can diagnose the problem.
I use Cura myself; it has nice visuals to not only see the model but also see the layers after slicing.