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.
It is definitely the tolerance in the customizer setting that needs fiddling if you have the same problem (depends on the printer), that will make the gaps bigger and less likely to fuse together. Higher tolerance means bigger gaps, but too much and it will be very loosely held together. Just gotta experiment with the tolerance setting.