I ran Audyssey and one of the first things it had me do was adjust my subwoofer to 75 dB.
As I tried to accomplish this, I realized that volume knob on the subwoofer was not doing anything.
It wasn't until I toggled the THX button (it was originally pressed in) that the volume knob started to respond. It was also immediately much quieter, which leads me to believe that it was at full volume before! The Kef manual only states that the crossover frequency control would be inoperative when THX was enabled, but I guess that applies to the volume control as well.
After completing calibration, I watched the video that I generated those samples from. Those trouble spots no longer caused distortion but I also noticed the subwoofer was much quieter than before. I did a quick Google to get some context and came across an
avforums thread where someone was complaining their subwoofer was too quiet after the running Audyssey. There were a couple of quotes that made me realize my subwoofer had been running way too loud previously (no wonder there was distortion):
Someone actually hinted at this earlier but it totally went over my head:
I guess I was expecting the bass to boom all the time but I don't have a subwoofer that's capable of that, plus that's probably not conducive to a proper movie watching experience. In my defense, I don't have much experience with home subwoofers, my only point of reference is back in high school when the point of subwoofers in my trunk was to be as loud as possible
.
TL;DR: Ran Audyssey, discovered that subwoofer was at full volume due to THX button, adjusted to a more balanced listening experience, distortion gone. Feel like an idiot but learned a lot and am happy. Thank you all so much!