Your scope as 70 MOA of total elevation adjustment with windage centered. That's 35 MOA up and 35 MOA down. With a 30 MOA mount like the the LaRue, you should be able to get to a 100 yard zero with your knobs, IF you actually had a flat railed M99.
I pulled up the current spec sheet from Barrett on the M99 and they are indicating that the rail has a 27 MOA slope built in. With that, things start to make a little more sense.
http://www.barrett.net/pdfs/Model-99-Sales-Sheet.pdf
You state you are running about 3 MILs high at 100 yards with glass bottomed out. That would be about 10 MOA high.
So. You've got 57 MOA built in to the rail and the mount. Your scope has 35 MOA. That puts you about 22 MOA high. Figure a couple minutes drop to 100 yards for the bullet, a few minutes for the scope height, plus a handfull of minutes for manufacturing variations and there you are, 10 MOA high at 100 with the scope bottomed out.
I don't like having my scopes bottomed out, EVER. So my suggestion would be to sell the Larue and get a no-slope set of rings. 27 MOA slope built into the gun is plenty for an M99. The mount just doesn't work for this application if you want to have a 100 or 200 yard zero.
Reason I keyed up on your post was I've seen this before. Had a new shooter at an FCSA match last year with an M99 he couldn't get on target with set of Barrett adjustable slope rings. Had about 30-40 MOA in the rings....thought the rail was flat...and couldn't figure out why he couldn't get on target at 600 yards with the damn thing. Pretty simple math. I took all the slope out of the adjustable rings and he was on target in 2 rounds.
-David
Edgewood, NM