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.
Could you provide more details such as: if you have modifications, replaced the RAMPS board with a non OEM board, checked the threaded rods to see if both Z axis switches are making contact with a fully seated assembly, etc. Sometimes one side could get out of alignment, and it won't make contact with the switch. You could turn the rod manually until it makes contact with the switch then start auto leveling again.