I know from experience with my powerful pellet rifles that if I shoot on a level plain, like my gun range, my pellet rifles need alot of increased trajectory as they really rainbow at 100 yards, about 4'-6'. When I shoot out of my upstairs window at crows, the rifles will shoot right on or maybe 2" low at the same range.
I had read in an article that the aiming up or down of a gun negates the effect of the gravity in comparison to a level field. It is true with my pellet rifles. Also, the misses could have been caused by habit we have of shooting a gun on a level angle, I had some misses like what you have described with my Colt black powder revolvers years ago where I was shooting high, on low fixed targets, I simply corrected and managed to hit em'. My arm simply was not used to the downward angle being called upon and had natural upward joint and muscle pressure.