I exchanged two emails with Chuck Westfall about this. I even pointed him to the threads on here about this. He chalked it up to the RAW converter:
"This sounds like more of an issue with the Adobe Camera Raw software, because there are no such issues when raw images from either the 1Ds Mark III or the 5D Mark II are processed in Canon's Digital Photo Professional software.
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I then wrote him back and told him there was a gentleman having bad issues using the DPP converter. His response:
"I am not suggesting that you simply give up on Photoshop in favor of DPP. Far from it! There are obviously multiple benefits to a Photoshop workflow that will never be matched by DPP or any other image editing program. On the other hand, it's been a reasonably well known fact since day 1 of Adobe Camera Raw that it does not render shadows from EOS Digital SLR raw images as cleanly as DPP. You can check on that with anybody who's used both programs. There is no doubt that Adobe has made great improvements to ACR over time, and by the same token so has Canon with DPP. Please understand that I am not saying that shadows in 1Ds Mark III or 5D Mark II raw images converted in DPP are completely clean. However, they are cleaner in the shadows than the same images processed in ACR 5.2/CS4. So, ultimately, what I am suggesting to you is simply this: convert the same RAW image with both apps and see for yourself. Once you've rendered a TIFF or a JPEG, then by all means continue your editing in Photoshop to get all the benefits deriving from that software.
For what it's worth, Adobe has always had access to Canon's raw image processing algorithms via the Canon Software Development Kits. However, they've chosen to go their own way, which is their prerogative, and completely understandable. Canon is in no position to tell Adobe how to design their software, just as Adobe is in no position to dictate to Canon. But the net result is that each type of raw conversion software ends up with its own look. The best I can suggest is that you try both and see which one you prefer. "