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.
Pleased you like them... it sounds like your slicing app and/or machine isn't dealing with the fine clearances quite as well as is required for it to come out with a free bar... so try 'uniformly' scaling up by 5%. That will increase internal clearances and should resolve the issue.
All the best!