It could only be:

1. Higher velocity of the leading pellets, which is what the chronograph would measure.

2. Lower average velocity of the ejecta as a whole.

The creation of the 'shot string' therefore must require energy. Frictional heat in the choke and the energy required to deform the pellets would seem to be likely candidates.

"The price of good shotgunnery is constant practice" - Fred Kimble