Factory barrels are button rifled. What this means is that a button is drawn through a bored barrel and the button finishes the bore and cuts the rifling. It is my understanding that a button is used for about 10 barrels and then discarded. If the barrel was cut with a new button, the barrel should be very close to spec on the + side and velocity should be fast. If the barrel was the last one cut with the particular button, the dimensions could be on the - side and cause slower velocity. These measurements will be in the .0001's of difference. This is what contributes to fast barrels and slow barrels. The velocity can often vary by as much as 150 fps. The first time I ever read about this was in an issue of shooting times magazine where they were talking about 7mm STW and the difference between fast barrels and slow barrels.
I am not sure if this is your problem or not. I would want to get some velocities from some other loads run through a chrono and then verify the drops with those before coming to any conclusions. As I have stated before, one of my chronos says 3175 with a 215 berger and the other chrono says 3075, but my drops show right at 3000. The drops are the important part. On the other hand, my gun with factory remington 180's shows 3350 accros my slow chrono and my handloads with 180 accubonds match the drops with 3350 as the velocity with 97 grains of H-1000 and seated to magazine length. I seat my bullets to within .010 of the magazine length and they still feed fine. The extra seating length lowers pressure and allows for more powder.