MakerBot Print is our newest print-prepration software, which supports native CAD files and STL assemblies,
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I didn't have this issue with mine. I think it might be because I set my extrusion width to .85mm. Sorry about that, I did not think it would matter. I just know its better to extrude a little wider then your nozzle. Give it a try and let me know if it works. I'll update the details.