Well in my case, I was shooting with a 5DIII, so is a problem with the new sensors. I never saw it on the 5DII.
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I keep all my RAW files in CR2 format, could that be the problem?
Yes, that's it - the solution is convert them to dng and check the "embed fast-load data" option, that's specifically made for speeding up raw rendering. You can still embed cr2 in the dng if you never ever want to loose the original format, though of course required hd doubles. Personally, I like dng since all programs I ever looked at (except dxo) work with raw dng nowadays.