Not to discount previous comments, but
I haven't seen that you centered the reticle in the scope between mounts. Could be that your first set up had moved the windage adjustment too far left or right to keep your elevation adjustment from being Max'd out. Since a scope is curved, when the windage is too far in either direction, the curvature of the inside of the scope restricts the amount of elevation adjust available.
Starting with the windage adjustment-----To center your reticle, turn the adjustment all the way in one direction, then count the revolutions that it takes to get it all the way to the opposite direction, then divide it by 2, and turn it back again that many revolutions.
If your scope mount has a windage screw adjustment, bore sight your reticle and move the mounts windage adjust so that the cross hairs are centered in your target. Or I use the vertical aluminum parts of my neighbors windows, to center the reticle in the bore. This should minimize the windage adjustment that you have to make with your scope, which should maximize the possible elevation adjustment.
If you have a weaver or picatiny mount, you probably don't have a windage screw, and must hope that all the holes and mounts line up with the bore.
Also, assuming that your bases mount to a common flat surface, you can measure the height of each of your bases with a caliper to check whether you bases will be parallel with bore, or of different heights.