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.
You have to set the z offset and auto-level probe positioning in your slicer or in the firmware. There are other setup and configuration considerations, too, but making sure the offset is set properly for X, Y, and Z will get you going. The probe locations have to take the offset into account. Say your X offset is 30 (that's mine using the SN4 sensor). You don't take that as a given. You have to set the left bed position to be larger than that. My probe locations are set as follows for bilinear probing: