Sorry for the delay, I have been swamped.
At 14' back with a +8dB boost in the 125Hz range, your amp will be clipping at anything over 89dB in this frequency range. Considering the dynamic peaks in home theater sources, I strongly suspect that this is what you are experiencing. Cutting the amplifier boost in half (from +8 to +4) will probably still sound quite good and give you much more available headroom.
The large dip at 125Hz is most likely floor bounce. If possible, you might try changing the vertical height of your center speaker and then re-running Audyssey. This might help considerably.