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.
Can you post a gcode file?
Also are you sure that you are in the correct coords (relative or absolute)?
I had an issue once with my mill that the program would set acceleration and jerk settings on its own a few lines after I set them, to values much outside of what the motors could do, and they would be stalled at the origin. could it be that?