OK, take a look at the unadulterated AV10 implementation of Audyssey (I did this with the AV10, not the iPhone app) USING ONLY TWO SUBWOOFER OUTPUTS. The problem is fixed! YAHOO!
I will still adjust the bass up a bit, but not 12 dB.
Now who's going to explain this?
I thought we did suggest that the way you hook up the 4 subouts may be the issue, as Audyssey is unable to deal with such a setup. As I mentioned, RC systems can only do so much, there are always going to be situations where the algorithm just can't resolve the issues they perceived from the data collected.
I would also predict, as mentioned earlier, that you could use subouts1 and 2 for the two SVS subs and subout3 for the Klipsch stack. Since the two SVS are located close to each other, combined them with just Subout1 like you now have done, may not make much of a difference, but it may, if you want to try.
Take a look of Gene (Audioholics) nice graphs I posted earlier. I will post a couple of mine, vs Dirac Live when I get home later, just to show what can be achieve. I must emphasize again then it does not mean a near straight line from 20-200 Hz will sound better than one that has +/-5 dB peak to peak fluctuation. At least to me, they didn't sound different, but that's just me. To you, a flat smooth curve may not sound as good as what you have now.
Edit: I don't remeber if Gene did that YT video review with how many, or any subwoofers. Have to re-watch it later.