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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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I've been fighting with this same problem ever since I switch to the new Marlin, I'm just about ready to switch back to the good ol'working ver 1 at this point I changed the tempwatch dog and im still having issues with it if the part cooling fan turns on anything less the 1 mm from the bed! keep in mind one of my printers has two thermal couplers and it not any better, my guess is, the new Marlin is better suited for more modern boards such a smoothie and duet perhaps