The way I back calculate actual MV from a chronograph reading is as follows. Set your ballistics software to out put in one yard increments, enter your recorded MV under the shooting conditions, edit the MV value upwards until your measured velocity is shown at the distance you had the chronograph from the muzzle.
I didn't see what velocity you were recording, but with that projectiles advertised BC of 0.419 at say 2949.4 fps recorded on a chronograph 10 yards (30') from the muzzle you would have 2961.0 fps at the muzzle. The atmospherics won't make that much difference to the output when your solution is only 0.1 fps in resolution and mearured over ten yards.
This method is acually very simple to do, just remember to reset your ballistics program or app back to ten yard increments afterwards, or you will end up with very large drop tables