Yeah, I'll have to verify my focus screen (EG-s in my case) is aligned properly. A while back I noticed that when I used AF the pictures turned out in focus but looked blurry in the VF. When they were sharp in the VF they were out of focus in the actual RAW file.
After re-seating the focus screen things looked much better. But if I'm going to rely on MF all the time, I'll have to verify that it's shimmed to be 100% accurate.
Thats scary. I had the same issue -- shouldn't these things just FIT? Shims!? Since when is changing focus screens a job for a technician?
This usually happens when shooting with fast glass having apertures in the 1.2, 1.4 range. I had the same issue with my Minolta 58/1.2 and Takumar 50/1.4 on my older 5D. Nice, sharp image in the VF, out of focus after downloading to the computer. I simply ordered a set of shims (Canon refers to them as 'focus screen washers') and made the necessary adjustment. Its a bit of trial and error, but the whole shimming process took about an hour or so. Before shimming, I had to do a lot of focus bracketing at the wide apertures...once stopped down to 2.8 or smaller, the problem went away. And the shimming will not have any effect on the camera's AF function, so no problems there.