Success! I did the following to solve my problem:
Turned down the sub volume on the AVR a little bit, from +9 to +4.
Turned the volume on my sub down from +5 to -7.
Turned on the Para Eq with a frequency setting of 30hz (the lowest)
A width setting of WIDE.
And then experiemnted with the eq level and settled on -6 (the lowest)
When I switched between -5 and -6 on the para eq leve I noticed just enough of a difference to know that -5 didn't sound "perfect" to me. But -6, though better, wasn't perfect either. I was wishing there was a -5.5 or something, but hen I remembered the Low Bass Adjust in the mode settings (music, movie, game) and thought that might solve my problem. So I turned on the low bass adjust, hoping that it would not change the way the bass sounded, but just make it a little more impactful. Voila! I settled on +2 on the low bass adjust. So I can yell you first hand that there is a difference to how the low bass adjust affects sound versus the para eq settings. Now Dark Knight and other material sound like they should.
Tell me how this would have been possible on a sub with just phase, corssover, and volume?
On source material that sounded great before these changes, the bass is definitely diminished. The solution for this is an easy one, volume. By turning the volume back up to the positive range on my sub I get the desired result, not a change in sound just volume.
Again, if the Bravus didn't have this feature (the remote) my problem wouldn't really be solved since I would have to get up off my butt and change the volume for different source material, but with the remote it is easy as pie.
I think the the reason why I had to monkey with these settings so much is due to the placement of my woofer. There is really only one place for it to go and I am sure that being in a corner and near a wood stove (an insulated one, don't worry I won't be toasting my sub) that I was just getting some crazy reflection, resonance, or whatever. Mind you I don't hear any vibration or rattling on the wood stove, but I think the bass sort of "echoes" in it if the sub isn't set up right.
I can't emphasize enough how impossible this would have been on any other sub. My previous sub didn't put out this kind of bass so it wasn't an issue. I originally purchased the Bravus 12D for better sound, thinking I wouldn't mess with the settings at all with the exception of the crossover. Turns out that the settings ended up being the coup de gras (spelling?) Had some people over last night as a matter of fact and was able to blow them away with some demos.
Thanks Aperion for making this great product and thanks for patiently answering all my questions and providing me with help. And thank you to all the forum posters for offering your advice and encouragement as well.