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 think this may be related to endstops and software limits in firmware. If possible try to home first, than try to move motor CW and CCW or switch off movement limits in firmware.
Or you mean they are going the same direction no matter what direction you sent them? That would be truly strange.