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.
What slicer were you using? Different slicers interpret tolerances differently; frustrating, but it's how it goes i guess! I've heard that reducing your extrusion multiplier can help, unless you can change your X/Y tolerance offsets somehow.