The sensitivity of the volume control and the equalization settings are different on these two models. Do you have an SPL meter? If so, then you can take measurements at 16/20/25Hz on the -2 MK3 to compare to the -3 MK2 to see how high the SPL level is before you start to hear the noise.
Are you hearing a whistling sound from the -2 MK3 port? Try putting masking tape around the entire port flare circumference to see if that reduces the noise.
Pete - Hsu Research