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I can't analyze your issue specifically, but your report may be a reminder to all who read too much about gear in camera forums and other similar places and get swept up in the early reports.
In general, even when newer gear offers improvements over older gear, the real value of the improvements is far smaller than the hyperbolic reports suggest. We read things like "camera X blows camera Y out of the water," "the difference is stunning," "X is miles better than Y," and so forth. In fact, X may be better than Y, but quite often by a smaller increment than we are led to expect and often in ways that don't really affect our work at all.
(To hear the initial reports we might sometimes imagine that new things are twice as good as old things. But with new things being introduced every couple of years, by now DSLRs would have to be - what? - about 30 times as good if that were true. They are better, but the increment is much smaller than that.)
In my view, the 5D3 is a great case in point. It is "better" than the 5D2 and is clearly a very fine camera. Canon did, more or less, what a lot of people often request - namely, take a good thing and improve it in areas where there is room for improvement. The 5D2, as those who actually shoot one know, is an excellent photographic tool that can produce truly wonderful image quality and which can work well in a wide range of shooting circumstance. It isn't perfect - nothing is - but it is very good.
In real world terms, the 5D3 is very similar in many ways and a bit better in others. However, if someone picks up a 5D2 and a 5D3 in twenty years from now and compares them, they will have to look very closely to identify the ways in which one is functionally different than the other, and they will regard image quality from the two cameras as being essentially indistinguishable. They are far more the same than they are different.