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.
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.