The color matrix and tone curve setting are only applied to JPG's by the camera. RAW files are just that--raw image data off the sensor. The white balance, color matrix, tone curves, sharpening settings, etc. are stored in the RAW file as tags, and Canon's RAW converter will use these as the default, but you are completely free to ignore the "camera recommended default processing settings" if you wish. I'm not familiar with Capture 1, but Adobe Camera RAW will use the tagged white balance settings as the default if the "as shot" white balance option is selected. I assume Capture 1 works similarly.
Regarding the autofocus question, was the camera on a tripod, or hand-held? If hand held, bear in mind that you could easily move a few mm between focus lock and the actual exposure. Also, how far away was the test target from the lens, how many times did you repeat the test, and what lens did you use? What was the ambient light level--the shutter speed, aperture, and ISO of the test shot(s)? Unless shooting macro, a mm or 2 +- on the focus isn't going to be very relevant in most real-world shooting situations. If you plan on picking those king of nits, be sure you have the camera and the test subject on a tripod or otherwise secured against any movement, and use either a remote shutter release or else one of the time delay drive modes to eliminate any possibility of camera movement. In general, I have found the 1Ds's autofocus to be faster and more accurate than focusing manually; the biggest problem I have observed is occasionally focusing on something other than the intended subject. I enabled the option to show the active focus points in shot previews; this will tell you what the camera thought it focused on.
