Wow, 3" out!
Never heard of this issue before. I would take off the mount and scope, put the irons back on and see if the rifle shoots straight, that would tell you if there is anything amiss with the barrel. If the barrel nut is not on tight that would explain a few fliers but not a 3" discrepancy in accuracy.
Once you have worked out if your barrel is at fault or not you can go back to your mount and scope and see which of those is giving you the issue. Burris and Leupold is top quality equipment though so I would be highly surprised if they are causing your issues.

Call Colombo, you need to do some investigating.