After calibration how come my focal length doesn't match what my camera or manual says?

The Calibrator does not have enough information so it guesses at one of the camera parameters. The basic answer though is, "it does not matter". What is important is the relationship of focal length to format width and height. You can take a camera and double the focal length, format size and principal point and you would have the same camera mathematically. The Calibrator will use the focal length information in an EXIF image file if available to scale these values but if there is no focal length data then the Calibrator will guess at the format size which may result in the focal length not being what you expect. As long as the Calibration metrics are good (low residuals, no correlated parmeters and small parameter precisions then that is what matters for an accurate result.