Some surprisingly large differences, as you note.
Which AF points were used for the "auto" shots? Or was it just "auto" where the camera's "AI" decides what you want to be in focus?
Did/would you get the same results if you just selected the central one, so you know at least what the camera is "supposed" to focus on. It was the first "customization" I made when I received the camera!
I recently checked the AF of my newly acquired 10D, but I have set my AF to use on the (most accurate) central square and it was spot-on at both ends of the 100-400 I checked ( with a bar-code on a vertical box, aligned at the 24 inches mark of a slightly inclined 4ft ruler, as the focus target). Focus was within 1/4 inch.... but I knew where the camera was supposed to try and focus. I used the closest focusing distance for this test of one of the most critical situations, using this as a macro at its closest focusing distance - like for the butterfly in the Member's Costa Rica gallery on this site. The 10D and D60 both focused accurately eventually, but the 10D is way faster, and its central square is a smaller zone (it will allow me to focus quickly on birds through branches that would have totally confused the D60) so I'm happy with my upgrade!
Andy