Ok, played around with the subs for a few minutes today while I could. I plugged in 1 Triad Platinum 18, level matched it, turned off Audyssey, put it in a spot I know is OK, and it sounded good. It actually made me appreciate it a little more after how anemic the twin S2's sounded.
I then thought something was wrong, so I just hooked up 1 of the S2's, level matched it, and immediately noticed something. Audyssey, when I had both S2's hooked up, had the level at -14 for both. With my SPL meter, I had the 1 S2 at -7. Both times, the volume on the sub was at the same point. This would be a great reason as to when they didn't sound so go, Audyssey had them down 14 db (-7 per sub). I have never had a problem when I have run Audyssey, every time I have run the levels it has been spot on. This leads me to believe I may have a mic issue. When I had started the Audyssey process, with the sub on the current volume setting, it would put the output extremely high, about 89db, where my SPL meter has it at 75 (hence the -14 db when it applies room correction). I don't know where to begin here, I may borrow a new Audyssey mic, or try running it again and see what happens. Maybe it was a fluke 1 time deal. Anyways, the 1 S2 played very well for the 5 minutes I listened to it, I am excited to get them both set up properly and see what happens.