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.
That's not like that in the design or been an issue for thousands of other people who have successfully printed this (refer to the images etc).
This will be a slicing app or machine specific issue. Unfortunately not all machines or slicing apps are as precise as others and with detailed designs like this with fine clearances that is all important.
A solution that often works is to uniformly scale all parts up by the same percentage (5 - 10%). This makes it less 'finely detailed' for want of a better term.
Hopefully this helps....