I am having the same issue, but the solution you use does not work for me.
Specifically, I am using a FlexiDually V2. I had trouble with it from day one. The ninjaflex jams on the second or third layer. I got it to work by turning up the temperature to 230 C and slowing way down to 10mm/s extrusion. I was able to print a large part (16 hours) with the slow settings. I tried to inch up on the speed (12 mm/s) but it did not work. Now I can no longer extrude NinjaFlex at the slower temperature either.
I was hopeful that your suggestion about recalibrating the extrusion parameter (Estep) may be the answer, so I tried to follow the instructions in the link you provided: https://ohai.lulzbot.com/project/extrud … libration/
However, when the free-fall extrusion started, it jammed about 40% through. I thought the recommended extrusion speed was too fast, so I cut in half (from 100mm/s, to 50mm/s) with similar results. I slowed it down to 12 mm/s and it jammed about 60% through. Then I tried to manually turn the gear and noted that it jams at about 40%. There is no back pressure since it is extruding into the air, well above the bed.
I took apart the drive mechanism (not the hot end) and found no build up. So I’m perplexed.