Maybe to help, I made a video which visually demos how chief calculates the pad elevation. Glenn's plans are more detailed but sometimes a visual helps to understand.
The video is a little long winded, because I'm just slow, but I think it covers most bases. I did discover a update problem which was giving strange results. This may be some of Scott's problem.
http://dl.dropbox.com/u/30269729/Pad%20elevation.mp4
MP4 file
http://dl.dropbox.com/u/30269729/Pad%20Elevations.wmv
WMV file
In any event, when Chief does update properly, the calculations appear consistent and correct. Problem is not in cals, problem is in correct updates.