Might be your EZ steps is off. If you measure 100mm of filament and run 100mm through extruder and are off by whatever amount use this formula. 100/(100-the amount you are off by) * whatever your setting currently is under control, motion, steps, E steps. So formula might look like this if you only got 95mm instead of the full 100mm and your steps are set at 95.7.
100/95 * 95.7 = 100.74.
Take the 100.7 and that is your new Esteps that you need to enter and store.
You want to test this both with your tuning and nut off first. Change esteps setting. Then put tubing and nut back on and actually have filament go through nozzle and test. Should be able to fine to it exactly. You might be getting resistance somewhere but this will tell you if it’s an extruder problem or tubing/ other problem.