Recently had this problem with a Browning X Bolt using their combined scope ring/bases with a Leupold VX-5HD. Problem was that the bases are different for front and rear, and there is actually an F and an R on the bottoms of the bases, but I did not know to look for that until I could not bore sight the scope. So, definitely check to see if your bases are different front and rear.
On the other hand, I had a Refield scope (at that time they were made by Leupold but not anymore; now made by Academy Sports) where I ran out of elevation on two different rifles using two different types of bases and where I was sure the base orientation was correct. When it happened on the first rifle, I shimmed the back ring thinking that something was wrong with the way the rifle was drilled/tapped. then later when moving the scope to a different rifle with different bases, I had same issue and figured out something must be wrong with the scope itself. I had an identical Redfield scope mounted on a still different rifle that was fine, no problems running out of elevation. So, sometimes the scope itself is just "not exactly perfect" and needs to be shimmed.