I have the same problem...
I am using 85mm f1.4 G and if the subject is close to me, say within 1m, the image will be sharp when AF is used. If the subject is further away from me, say 5m, the subject will be out of focus if AF is used. However, it wasn't the case if I manual focus on the subject.
I had the camera in to service center today and they told me that the CCD is the culprit.. I am not 100% sure.
However, if only one of your lens has the problem, the chances are that the lens' misalign inside... you probably can't see it... but they had to re-align to its "original" factory setting.. it is not user servicable... basically it involves removing all lens part and fit it back correctly.
Hart