First, eliminate problems like a loose base or some assembly problem. If there is no problem then:
Tac-One, what distance are you sighting in at? Going out on a limb here, but if its quite close, like 25 yards or less, the barrel being beneath the scope, the bullet starts out low, crosses the line of sight traveling upwards around 25 yards, and then starts its arc downward to cross the line of sight again somewhere out further.
If you sight in initially quite close, you may find that close up, you can't get the point of impact up high enough. If so, don't worry, as you move the target further back, the bullet impact point gets higher. At 100 yards it may be over the target and you have to bring it back down. That's the way it is on one of my guns. Zero at 100, but quite low up close, because as you mentioned, the scope sits high.