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.
The tolerances on the pieces are very tight as they do tend to loosen up over time. Tolerances are printer dependent, so even though they work well for me, they may not for someone else. Here are two solutions though.
Scale the pegs and pieces down uniformly by a very small amount in your slicer. I would guess that 1-2% would be plenty.
Let me know if this works.