I have messed around with this as well. What I have found in visiting with the guys I shoot with about this is that sometimes there are differences in how we measure. Not a lot, but some.
Pastor Steve, I haven't ever had a bow that liked a nock set that high, but that doesn't mean it won't work for you. Then again, I don't shoot 3 under either. If it ain't broke, don't fix it, I'd say.
A young lady that we shoot 3-D with pretty often shoots 3-under. She got a new bow and showed up at a shoot with it set up with over-under nock points and was shooting 3-under with the cock feather in. Everyone (but me, I know better) was ribbing her a little about the set-up... until she shot a near perfect 3-D score and SMOKED everyone else. Then they were real interested to take a look at her set-up.
Do what works.
Good Luck,
OkKeith