Re: Question re: optic set-up
rhutch,
That's a Zeiss Diavari 3-12x56 T on board, right? According to Zeiss it has only 36.7" of adjustment. That's 18.35" up or down. Somehow you "lost or used up" all 18" of your up adjustment. How much windage adjustment (L or R) did you use to get sighted in 6" low @ 100 yds? Using a lot windage adjustment can limit your elevation adjustment.
Either your rifle, base, rings, or scope is introducing 24 MOA of upward cant, rather than downward cant like that produced by a 20 MOA base. Normally when a bullet leaves the barrel it crosses your line of sight (LOS) twice: once on the way up and again on the way down (or rather right on your LOS when correctly sighted in to be dead on @ 100). In your case the bullet is never crossing your LOS. It starts out in your barrel, 1 1/2" to 2" below the LOS (and your scope), and finishes 6" below LOS. Think of it this way, your LOS is level, your barrel is pointing down...not up.
If this were my rifle, I would begin by doing Trouble Shooting 101, by changing something. The easiest and cheapest way is to contact your custom base maker and explain your problem. Maybe the maker will agree to swap out your base for another, as I suspect the base maybe the culprit.
Failing that you could spend $50 or so and buy a pair of Burris Signature Zee Rings. These will allow you to "get back" the 20 MOA you lost by allowing you a full 20 MOA of down cant. If it is the receiver rather than the base again your custom base maker can help. I notice you do not mention the makers name?
Other than that I'm fresh out of ideas...
Best of luck,
Bob