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 only thing that sticks out to me is you both seem to be printing at pretty low layer heights and you both seem to have a problem. Mine was printed at .2mm layers height. While I do remember having to bore out the PCB mounting holes, I had no problems biting the screws into the plastic to secure the two halves together.
Are you possibly under extruding? Maybe find a calibration print on Thingiverse and test fit 3mm bolts into it to see if the calibration is off?