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.
I regulary print at speeds arround 80mm/s. Retraction is set to retract 4mm at 40mm/s, EAccel is set to 1000mm/s^2. It seems to me this is not problem raleted to extruder. Have you tried another fillament?