I had my panel replaced and the difference was as clear as night and day.
I want to note that the pops out of the box (common pops), and the flashing/fluctuating black levels are different phenomena. This is clear, at least to my naked eye and explains why only some of us see it.
The logic fw update took care of the "common brightness pop" on my first panel, but I was left with unstable black levels in certain material, and especially on digital video files.
The black level performance on my new panel is far better than on my first panel after the logic update; solid, including on material that used to fluctuate/flash. There has also been a large improvement in 3d content, which was full of pops before and after the logic update on the first panel. My first panel was no doubt a lemon.
This leads me to believe that some panels have a defect in addition to "common pop." My new panel had the "common pops" but after I did the logic update they were gone, and the flashing/fluctuating black levels were not present in material that showed them on my first panel. The PQ of the new panel is far superior.
Maybe the problem lies in the itoless panels. My first panel used the itoless file. The second panel used the ito file. From what I have gathered ito is a material in the panel, and it is expensive, so itoless panels have been produced. I will keep an eye out for the return of this problem.
I am pretty much happy now. The e series is not as bright as the d, so daytime viewing on the d series is better anyways. Now that the picture looks how it should have all along, I do not want exchange it unless the pops return or something else goes wrong.
Just make sure you do the logic update to your new panel and you will be good to go. Downgrade the firmware if you have to.
THE ALL MIGHTY MACACASIAH HAS SPOKEN!