When I let the SMS1 perform its self-EQ (having first adjust the H + L average to around 80dB) the repeating bursts scare the hell out of me by first starting with a loud speaker rattling noise...is there any way to exlude < 20 or 25 Hz before the test starts?
What I hear can't be healthy on the sub...

You might try adjusting the subsonic filter on the SMS-1. The default is 15Hz, but I have mine set around 20Hz instead. That may not help with the self-EQ test tone (since it's generated inside the unit and sent straight to the sub), but it would help with the auto-EQ and manual adjustments.

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.

Thanks Jeff,
No it wasn't, as I found out today when switching the sub for my REL Strata.
The REL does not rattle!
So it must have been the Q2 dipole sub, the two chassis (which happily fire directly at each other across the output port) seem to have some trouble around the lowest fq, or something...