All, thanks for the reply's. Some clarifications:
@PENG
1. When you ran Audyssey and got the polarity error, did you have the pre out of the AVR connected to the Elac's RCA input?
YES via Front RCA/PRE
2. If you did, then why did you say "nothing connected".
Because there is no 'speaker' cables connected. Front L/R speaker terminals are empty.
3. During the Audyssey run, in the first main listening position, did the front L/R make any sound?
Yep, via the PRE
Okay then it is clear, Audyssey detected a polarity error that may be legit. Audyssey does not care if the speaker terminals are used, it detects polarity by analyzing the phase relationship between the speakers picked up by the mic. It is not an electrical wiring detection, but an acoustically based detection. So as long as the speaker is making sound, it doesn't matter if the AVR's internal amp is powering it, or the external amp via the AVR's pre out. Either way, Audyssey can and will do its job just the same.
You should check and make sure that the interconnect's leads/wires are connected/soldered to the RCA connectors correctly. I know by experienced that this could happen, though rarely. I had a couple of those that in fact had polarity reversed in the connector at one end. I had to open it up and re-solder the leads to the connectors correctly. You can check and verify that with a multi-meter or open up the connector for an visual inspection. If you don't have one or don't want to be bothered, then you can simply replace the interconnects in question, but be sure to replace them with something from a different brand, in case any such defective samples may be from a whole batch of production. Again, this scenario is not likely, but it could happen, and did happen to me once.
If you can confirm that the interconnects are wired/soldered correctly, then you can choose to ignore it or try to play some stereo music that you know have very focused center stage, such as vocal. In stereo mode, without the center speaker, the vocal should sound right in the middle and planted securely. The sound should not appear to wander to each side or from the sides. If the center stage is not securely planted, then the polarity is reversed somewhere, likely within the internal connections of the powered speaker. In that case, it will be up to you to choose ignoring it, complain to Def Tech and see what they can do, or just fix it yourself.
Hopefully, the best outcome is if one of the interconnects has the polarity reversed at the RCA connector, then it is a simple matter of fixing it, or replace it with another interconnect.
Would Marantz really allow it to stress itself? If so, what is the purpose of having PRE's & SPKR outs. Marantz also does not have any user configurable "Output On/Off" settings. I am hoping that somewhere in the AVR logic, it see's no load on those SPKR terminals and doesn't expend any energy unless something gets connected. Also, wouldn't this be an issue for unused channels? i.e. Only using 5 vs 7,9,11, other channels are simply not connected.
I think you misunderstood his point. You asked if the AVR still send/use power if the pre outs are used instead of the speaker outputs. The answer is, yes it will use power but it will be less, because only the processor and the preamp section will be used, and the power amp channels not actually driving the speakers will be just idling. In other words, those amp channels will use just consume a little when idling. As slippery mentioned, the transistors will be drawing quiescent currents. They will not, and cannot send power to the speakers simply because the speakers are not connected to the binding posts. So no, the Marantz won't allow itself to be stressed at all. The preamp/processor part will work the same way but the unused power amp channels will only consume the much less idling power.
But if I am not having to amplify 2-channels because it is being handled downstream via the PRE out, the overall power consumption should be less.
That is correct, obviously.
