The OP said at the get-go that he was covering the center of the target with the sights. I don't think holding too low is the problem.
The solutions are always that the guy is aiming with a 6 o'clock hold, or is gripping the gun wrong.
Sometimes guns will hit lower (or higher) than the sights, even if you are doing everything correctly.
S&W, Ruger or anyone else making guns today can't have the gun leave the factory and have them dead on for every individual or a certain load, etc. You just have to experiment until you find what ammo is most accurate in your gun, and whatammo hits where you aim.
With adjustable sights, no problem, just a few clicks of the rear sight.
With fixed sights, you need to try a different weight of bullet, or if you don't want to switch weights, you'll need a different height front sight.