This is a case where "assuming" made an ass out of me.
I simply haven't thought about how Shooter handles distance to chrono.
My process is to place the chono @ 15 feet and run the data on JBM Ballistics, which gives the velocity @ the muzzle based on distance to the chrono.
I then use that corrected velocity in Shooter. Then fudge it as needed, along with bc, to Shooter to match actual drops PDC (pretty darn close).
I think this is another point in favor of the Magneto chrono thing or the acoustic gizmo down range.