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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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I have same problem. Solved it with a geared extruder. I use this: https://www.thingiverse.com/thing:2172854 or you can choose one of the many Greg's Wade's Geared Extruder variants...

Drakon Geared Extruder