Converting the values we get from an instrument into meaningful numbers in standard units is called calibration . For example, I keep my alarm clock at home set to the correct time, but my spouse keeps hers 5 minutes fast. When we make scientific observations we make the same sorts of adjustments, though the errors are not usually voluntary. Think about an image of the Sun that falls on a CCD camera with a million pixels. Or if we compare pixel 951 with pixel 952, they may give different readings for the same solar brightness - the sensitivity is different for each pixel.
Most people find pictures of the flat field are kind of boring.
You can probably imagine all sorts of problems that could introduce errors in a measurement of the Sun's brightness. The biggest problem in the MDI instrument is that the wavelength filter isn't quite the same everywhere. Other annoying problems are due to the way we have to observe things. For example, if you observe the Sun at noon in winter it won't be as bright as it was in the summer. The intensity isn't different because the Sun changed, it's different because the winter Sun is lower in the sky.