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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I measured them, 10mm was not long enough.

Maybe its the printed parts.

What profile did you print with? Did you scale at all?
I print with a 0.5mm nozzle, used the fast/low quality, used ABS, and didn't scale it (ABS can shrink a little but I expected that you accounted for this).
The dimensions seem spot on when they interact with beam and other parts; just things around the M5 screws seem a little off.

Did I mention that I am excited by this upgrade! ;-)