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MakerBot Print is our newest print-prepration software, which supports native CAD files and STL assemblies,
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I think it's cured now. I'll leave this here in case anyone else has the problem. It appears that there is now a setting in Cura to switch between fans if you have multiple extruders. In the settings/printer/manage printers/machine settings/extruder 1, make sure the fan number is set to zero.