It could be that 100mm/min is approaching the limit for how fast the hexagon hot end can soften 3mm filament. I reached that conclusion in the Estimating a Feed Rate Limit on Extruder E-steps Calibration post in the Marlin Motion Related Configuration.h settings for MakerFarm i3v thread. See if you get more consistent results running all the tests at 50mm/min.

Note that you can also run the test with a cold hot end. Remove the hot end nozzle so that the 3mm filament can pass through the hot end and start your test with an M302 command to enable cold extrusion.