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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.

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Problem solved. Marlin configuration for extrusion rate was wrong ( larger than default) reducing this value solved the problem.

On the lower cubes it cant be noticed because the extra material extruded merges with the infill.