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.
There is definitely something wonky with your setup, but I have no idea what. I have no idea how I would even be able to duplicate that bend you get even if I wanted to. I have 5 walls, 1mm top and bottom, usually 25% infill. I presume you aren't printing with ninjaflex :-D