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.
your x or y axis motor wiring is reversed causing it to think it is printing the right way but yet the motor does the exact opposite. Remember that you cant just flip the connection to fix the problem, you also must go into the firmware and change the endstop settings or else the motor will drive the carriage into the opposite end of the printer. Or as TBRlshtar pointed out you can also tell the firmware to inverse the logic on the X (or Y) direction.
A quick way to see if my theory is correct is to go into the software of your choice that has manual controls (i.e. pronter face) and tell the printer to move left, right, forward, and back and see if the response is that of which you expected.