I noticed the other day (on my OmegaView 45D) that I could get the top bubbles level, but then I spun it around 90 degrees on the tripod head pan and it was off (I've got the upside-down A-S Monoball P0, pan on top of ballhead).
Turns out that there's some sideways-play in the clamp that clamps twixt the tripod head and the rail.
Easiest way to calibrate is to set all the standards to default, no shift/tilt/swing. Take the camera off and level the tripod head (I've got a circular-bubble on my A-S clamp). Put the camera on and then level the top bubbles using aforementioned clamp. Now I know that the top bubbles are square and true to the tripod-head bubble (at least, until I move that clamp or change rails).