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.
What suggested JCriotz may solve the problem. If it will persist, there may be some problem on the X and Y motor connector or stepper driver on your electronics. Try to pull the stepper drivers out and and push them back (maybe also swap the drivers).
Also check by hand if there is the same friction when moving the carriages there and back.