First - to be clear - are you saying that you recorded MV's from a load you worked up in QL - or are you just comparing data from QL with data from a reloading manual?
Second - look up "cross sectional bore area" in QuickLoad instructions - then do that. You will have to slug your bore, then measure the number, height, and width of the lands, and your QL results will be more accurate.
Third - double check everything, including case H2O capacity.