MakerBot Print is our newest print-prepration software, which supports native CAD files and STL assemblies,
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You might try scaling the pins that hold the gears a little bigger to see if the helps. I know that I went through several different sizes myself to get it just right. With different printers having different tolerances, there may be a difference in what works for your print.

I use the free version of netfabb basic to do my scaling. With it I can scale each axis independently, and it has great repair tools.