It has been my experience with my Encore and (and I can show you the paper targets to prove it) that I will inevitably shot low on shots 25 yards and in. I know physics says no, but I can shoot at 25 yards and be 2-3 inches low (3 shot groups), be 1inch high from 50-100 (3 shot groups) and be zeroed at 125 yards. Gun has always performed that way. Come to think of it my old 45cal Hawken would do the same thing.

Sounds about right if your scope is 3" high. Whats your scope height? maybe your front scope height is taller then the rear??
What load setup are you using?

you did the right thing. congrats and nice buck