I can't say I'm a ballistics expert,but I know something that might explain your observations. Have you heard of "Convective turbulence"?
You see...I helped my dad get his private pilots licence by making study tapes for him and I learned a few interesting things.
Different surfaces absorb, release and radiate heat very differently, providing lift or downdrafts.
For example, hot tarmac on a sunny day gives great lift, which can be a problem while landing. An aircraft going from vegetation to the beginning of a blacktop runway, can suddenly gain ten or twenty feet of altitude in a second, and it can screw up a landing causing overshoot, or if the pilot overcompensates, or foolishly tries to make the landing anyway...can result in a crash.
Conversely, if you are flying low over a large parking lot, or sandy area, you have artificial lift, which can disappear when you reach vegetated area, or turn into negative lift over a body of water, plunging the plane into powerlines or other obstacles that you thought you had enough altitude to avoid.
These problems can be magnified if you are in a bank (turning) while making transitions from one land type to another because of reduced lift and altitude control while banking.
Could these "Convective turbulence" effects perhaps start to explain your observed loss of accuracy? perhaps it isn't the moving water itself, but the transitions from hot/cold/hot air, that are disturbing the flight stability of your bullet.
I mean...if a hot road, or a cool pond can make an aircraft weighing several thousand pounds drop ten feet in a single second...perhaps one or more of those transitions can seriously affect accuracy, by a few inches or more?