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 have a feeling you missed this from the Readme.md file:
This is where the settings are stored and it won't run until that is set before the compile and load.
[this is done in the Arduino IDE under Tools -> Flash Size...]