Hi leatherneck,
When you change to 3 under, the tail end of the arrow is the width of the arrow higher, approx. 3/8". With the same anchor point, same "point of aim", the arrow will hit lower.
I shoot instinctively, & learned to "shoot the arrow", not the bow. So either I don't have the same experience, or I adjust without thinking about it. Mayhaps comes from experience, dunno.
So I have to ask if you're gap aiming, or using some other method of aiming other than just focusing on a spot. If you are shooting instinctively, then with practice it will likely come around in a short time. Hope this helps some.
All the best! - Q.