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 haven't had any problems with it binding or layer shifting on any axis. Some things it could be: heat bed wires getting caught on something during printing, loose grub screw on the motor shaft, over tightened wheels, over tightened belt, over tightened idler pulley, bad bearings on wheels or idler pulley. Try removing the belt and sliding the build plate by hand. Also it would be cool to see the build, no one has posted a build yet...