I know this is an Old thread, but I am now having this issue.
Here is what I have found.
It seems to only be in sunlight or with the hot shoe flash.
I have ran 400 ss so I know it isn't motion blur.
I can take the camera into the studio and get AMAZING photos...
Only other thing I have noticed is the DOF seems so shallow compared to other Canon cameras.
I can be at a 7.1 or even 9 f-stop and from a persons nose to ear can start to be out of focus...
Or in sports a player carrying a football the ball is in focus while the face is so soft.
I check settings from old photos and I was even running lower F-stops with more DOF with the 1Ds mark II and 1D Mark II
Anyway, I hope Canon or someone can continue to figure out this problem as it would come and go, but now it is HERE and wont go away for my Camera. I guess I will call Canon in the morning and see what they have to say....
It is a basic fact of photography that larger sensors achieve a shallow depth of field.
Some like the deep depth of field that they had with their tiny sensor in a point and shoot, and just plain hate the shallow depth of field in a FF DSLR. That's ok, but the only answer is to go back to the point and shoot, or use very small apertures.
You also need to understand that distance to subject has a huge effect on depth of field, so if you get up close, depth of field is shallow. Combine the two, large sensor and close distance to subject, and the shallow depth of field can be wonderful, or awful depending on what is needed for the image.
If you want more depth of field for a portrait, use 85mm - 200mm, some even use 300mm. Don't use 35mm and compensate by getting close.
Here is a image at 35mm at near mfd. I like the effect, but maybe not for a portrait.
On the other hand, here is a portrait of my son with a 135mm Lens at f/2.5. No problem with depth of field. Its a matter of lens selection to get the effect you want. The subject is standing away from the background so it will blur.