Coop,
The Red Dot Sight can be considered a "Zero Power Scope" that uses an image of a red dot, projected at infinity instead of cross hairs.
If your gun was right on at the shorter range and shot hi at the longer distance, with no sight adjustment, it sounds like the bullet is still climbing when it hit the more distant target.
Many Red Dots, mine included, have a lag in the mechanism that moves the location of the Dot. If yours does, and the last adjustment was in the opposite direction from the direction you want to move the Point Of Impact, you may well have to put in 8 clicks of down followed by 6 clicks of up just to get the desired change of "2 clicks down".
This applies to windage as well as elevation adjustments. Iron sights may have a slight (or in some cases, a large) amount of play in them. My Ruger KMK678GC had a slight amount of play so I changed to a Millett Iron sight and it has almost none!
If you have any more questions, feel free to contact me off list at: Mailto:jfl@pcmagic.net
Good Shooting,
John Lipscomb