MakerBot Print is our newest print-prepration software, which supports native CAD files and STL assemblies,
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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!