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.
Both seems to me as firmware related problems.
Thermal regulation went crazy when I messed up with thermal runaway protection.
Strange behaviour of steppers is mostly due to some wrong settings, or missing/malfunctioning endstops. You should home the printer before any test movement.