I got my first Ruger earlier this year and had the same problem with the rings. Sadly and to Ruger's shame, their owner's manual says nothing about scope rings being different height. I put them on wrong at first and thought they had included horribly mismatched rings with the rifle. If memory serves correctly, the low, or short scope ring mounts on the front of the receiver (closer to the muzzle) and the higher ring mounts towards the rear.
Also see my reply on an earlier post, 77 Mark II Scope Ring Fit, last edited July 9, '06