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.

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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.