Assuming the same POA, all rifles will shoot to a different POI at 25, 50, and 100. The difference is more noticeable with high mounts.

Hey Droptine - your problem is simple. You just need to sight your gun in.
When you sight in, you need to shoot at a target that is far enough away to be near the crest of your trajectory. 100 yds seems to be about right for most calibers and most shooters. If you sight in to be say 2 - 3" high at 100, you will NOT be higher than that at 150 or 200. If you sight in at 50 yds to be "about right", you'll have no idea what will happen downrange.