When this kind of cogging problem has happened to me in the past, it was incorrect motor parameters. Maybe change your max speed setting from 90hz to 60hz and see if that does anything. I wouldn’t think that should cause it, but maybe the latest firmware is calculating the V/f ratio based off of 90 and not 60 like it should. If that is the cause, might explain why auto tune is not working.
Since the problem got better by changing the S curve, it sounds like the auto torque boost might not be working correctly. Parameter A041 is set to auto in the parameters you posted, switching that to off might work too.
Since the problem got better by changing the S curve, it sounds like the auto torque boost might not be working correctly. Parameter A041 is set to auto in the parameters you posted, switching that to off might work too.