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 you're having issues. ... this all comes down to your machine and/or slicing apps accuracy. . As it sounds like your machine is not able to deal with the fine clearances try uniformly scaling it up about 5% as that will increase the internal clearances. I hope this helps.