So... You're seeing a difference in accuracy dependent upon where the dot is positioned within the reflector pane (sight window)?
Is it a difference in precision - group size, or difference in accuracy - POI? If you're shooting on target with the dot near the bottom and not when centered, then you simply need to re-zero. If it's a difference in precision, meaning it shoots 2" groups near the bottom, and 4" groups near the center, then you have something very funky going on.