Your loading process sounds fine and not the source of the low velocities. Individually weighed charges, proper OAL, and components that match the load book don't leave much room for error.
Any concerns about your chronograph? Maybe load and shoot a few more of your 45 LC's and then shoot them over the chrono alongside some other rounds with known velocities to rule out the chrono as the problem. Perhaps you could shoot a few rounds of factory ammo and see how close you come to the published velocities.
Chasing strange velocities is a pain. Best wishes.
