Such things can happen. Have had it my self as well. Auto tune is just a heuristic approach as you already see with the many possible equations to select from. It can also get worse if the temperature readings are not smooth - also we already smooth them internally. Make sure max pid is 255 and that you do not constrain I gain too much:
/** \brief The maximum value, I-gain can contribute to the output.
A good value is slightly higher then the output needed for your temperature.
Values for starts:
130 => PLA for temperatures from 170-180 deg C
180 => ABS for temperatures around 240 deg C
The precise values may differ for different nozzle/resistor combination.
Overridden if EEPROM activated.
*/
#define EXT0_PID_INTEGRAL_DRIVE_MAX 205
when that is lower then what you need for your temperature you will get exactly your effect as well. Should be editable in eeprom so just check what it is set and increase it and see if it improves.