At one time I had a rifle, can't recall the brand or model now, that had different height bases for the front and rear. Not a problem except the mounting holes location allowed them to fit in either position. Of course on the first try I had them reversed from what they should have been and I don't remember if I was shooting the ground or hitting the sky with it, but it was one or the other. Reversed the mounts and all was fixed, gun shot and the bullet hit where the crosshairs were!!!
Mayby check to see if that may be part of your problem?