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.

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That's interesting, now I have to measure mine to see. Seems like it might be an issue with the base, I've noticed that mine is spaced slightly different than what it should be vertically. There is a new version of the base in the works that may help with these issues, too.
I'm glad to hear that the 90 degree orientation works