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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Just had a thought now: did you reconfigure your firmware to not send beep signals to that 27th pin? As it beeps at every move and confirmation of the menu system maybe it still sending the beeping signals through that pin an that is causing the issue!!