I've read this entire thread and keep going back to two points that the OP has mentioned. One being that he is listening to music or getting clipping (on the subs) at 80% on the volume dial on a $6k integrated with around 400 watts going to VERY efficient speakers. I would guess that this system (if set up correctly (and I mean no disrespect to the OP by saying that)) at 80% volume would be concert level DB and literally chase anyone out of the room rather quickly. So I'm wondering if possibly either the input signal (source) is abnormally low that the NAD has to be turned up so much that the output to the sub amps is clipping? (for instance when streaming from my macbook, i occasionally have the volume down on the macbooks output to my dac, which in turn causes me to turn the volume up to abnormally high on my preamp to get the volume I need) Could there be some settings in the NAD's system that are not correct? Possible some partial muting or something like that? Have you tried a different source, streamer, cd player, etc? In reviews of the NAD I have not read anyone having concerns that it has to be turned up an excessive amount to get adequate volume out of it. The second point, and forgive me if I have missed it along the way but it sounded as though the wiring or phase of the subs was in question. Correct me if I am wrong, but one woofer is facing front and one facing back. One of the woofers 'should' be wired out of phase with the other so that an input signal pushes the both woofers towards or away from the listener simultaneously regardless of the woofers orientation in the cabinet, right? I thought the OP said he had them wired so one was firing forward and the other firing opposite. If that is the case I would guess that would cause the original issue all in itself. Also, if they were wired this way, (opposite) and the OP went to correct the issue WITHOUT correcting the servo wiring on that woofer we can see how this would cause an issue as well.
