You may have an area of a spot where the specified background level is above the actual image intensity. In this situation, the background level must be restricted to the image intensity level of the area. If this did not happen, you would effectively lose volume from areas of the spot where the image intensity is above the background level and your analysis would not be in accordance with good laboratory practice. When I load my images into Array, their resolution appears to be reduced. Actually, no, it won't affect the analysis at all.
All analysis is performed at full resolution using the original image.
Future versions of the Array software will allow you to turn this optimisation off. Before doing Intensity Calibration, you had performed Quantity Calibration and had added a number of low-volumed spots to a curve. This was not a problem when you were actually doing the Quantity Calibration as the software would have warned you in the first place. However, once you had performed Intensity Calibration, the spots' 'raw' volumes were recalculated and two of the spots you had added to the Quantity Calibration curve now had the same raw volume. This meant that there would now be more than one calibrated volume defined for that raw volume - a situation that cannot be allowed if the curve is to remain valid.