Simple...CR's methodology is incorrect. They survey their own subscribers. The only way to have a meaningful survey like this is if it is completely random. Survey people from all different demographics who bought a new car. Different regions, different ages, different income levels, etc. CR could care less whether or not 90% of their subscribers drive a Camry (probably close to reality anyway).
A similar scenario would be if someone surveyed what midwesterners preferred to drive and extrapolated that out to the entire country. I'm sure the average west coaster would not drive the same thing as the average midwesterner...but that is the same flawed logic that CR would use...hence why it is worthless.
The JD powers IQS survey is WORTHLESS because it just surveys the first 90 days of ownership. I don't think any company that couldn't screw a car together to hold for the first 90 days should be in business here. It's even worse now with the subjective "ratings" as half the stuff reported is probably things the buyer knew ahead of time but bought anyway and still decided to whine.
The 3 or 5 year long term quality survey of JD powers is much more important. It's pretty much a given that it will be more accurate and reliable than CR due to the correct methodology (random samples)