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 was having this issue too with my Dremel Idea Builder. Because the author included the original sketchup file I was able to resolve it. There was some funky modelling going on at the bottom of the stair.
I'm finishing up the first floor print today. If everything goes as planned, I'll be posting my remixed files for this with a few changes. (like a notch in the 2nd floor roof so it doesn't conflict with the chimney)