Ok. This may seem really simplistic, but since you did not describe your set-up here's a consideration.

Any chance the "noise" is simply the sub vibrating in (uneven) contact with your floor?

In my case I had one of my subs sending out one heck of a racket when I first used the SMS-1. I pulled the driver, checked-out the internals and screwed the driver in nice and tight - but same thing happened. Then it clicked: the sub's feet have metal "pads" on them, and the sub sits on a bare concrete floor - which is never perfectly even. So one of the feet was just harely touching the floor and voila! Vibration like crazy - that sounded just like a blown driver might.

Some felt pads later and the problem went away completely.

Perhaps yours is a physical problem such as mine was.

Even if your sub's response does not extend down to the lowest sweep frequencies, instead of sounding harsh in should simply not reproduce the sound (to the same level as the upper frequencies.)

Regards.