RE: Mossberg 500 problems?
The odds of both those guns having the same thing wrong with them and one being a 12 and the other a 20 is HIGHLY unlikely. And if this was the case a gunsmith should have noticed it immediately and either fixed it or not done the work and let you know about the problem.
Without actually seeing the weapons I doubt there is much any of us can do to help you. I really suggest trying to have someone else look at them. Tell them exactly what you had done and what is happening.
I can think of something else though. If you maxed out your scope adjustments there is a possibility you could have ruined your scope. I have a buddy that did that before.
Having your rear mount lower than the front will cause it to shoot low though, I just can't see both guns having the same problem.
Paul