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.
I did a poor job of explaining the face sizes, and cindybee's reply seems to point to that being the problem.
What Joe said :) Assembling the cube on a tabletop or in the palm of your hand without the pins is the best way to initially line the pieces up correctly. The difference in the face sizes on the cube center are pretty subtle & easy to confuse (Ask me how I know :) ).