Hi, even using Raw format the files shouldn't be 'adjusted' to make significant changes to the exposure that you made. The whole point of Raw is that you are in charge.

With the correct prevailing light levels you should be able to get somewhere near a good mid-tone reproduced from a grey card while using a 1/60sec exposure and an appropriate aperture. If the camera is correctly adjusted it should, a far as is possible, reproduce the tones as they appear in a scene, in this case a grey card, correctly - otherwise there is not a lot of point to an exposure meter!

If the camera gives a correct exposure at 1/60sec by the time you are shooting at 1/1000sec the grey card will be four stops under exposed but there will, as you have found, still be residual exposure and some noise etc - that accounts for the figures you are getting. Unless you are a scientist involved in camera development I wouldn't fret about that.