First things first. The program that you are using is a guide only and is algorithm based using complex formulas. These formulas were derived based on testing conditions in the lab. Things like wind, atmospheric pressures, temperatures, rifle twist, condition of barrel, consistency of bullet, powder/primer/case trimming/bullet seating also can play a role too. You are relying too much on the theoretical model in the program.
All reloading manuals provide pretty good estimates of the muzzle velocities of their bullet with a specific charge of powder. What you are doing, is to attempt to back calculate (the hard way, i might add) your velocities based on bullet drop. If you want absolute certainty of your velocities - buy a chronograph.
Using your method to determine velocity is kinda like guessing the speed of the vehicle in front of you on a highway using a stop watch and timing his travel between two power poles 500 meters in front of you. When you could instead, just keep up with him and use your speedometer as your reference.
I shoot a 243 and use Nosler 70 grain bullets exclusively. I worked up a load based on muzzle velocities using the nosler manual and use 335 powder. It's a tack driver and the load is very consistent. I then shoot to determine the average drop of my load at different distances and plot my curve on that basis, not the other way around.