This diagram illustrates what he is saying:
https://cdn.britannica.com/30/178630-050-D12B8390.jpg
Guys, I get it. I was just trying to get the OP to be able to figure out what the problem might be. I did not run his 9mm through any ballistics tables to calculate the trajectory path.
I usually sight my 9mm 16" PCC's at about 1" high at 25 to get them pretty close at 100. I'm using red dots or open sights.