I believe Brian is on the money in a couple of ways. First, make sure your scope height is very accurate. Then, as Brian suggests, use a hundred yard zero. I like it because all of your dope is in positive numbers, you are not starting with negative drops at short range and changing to positive at longer. That will give you an idea of what the bullet is doing as it goes downrange. With a 3" high "zero", (it isn't a zero if it is 3" high), there are a lot of variables to deal with. Namely, are you really 3" high, or almost? Get an absolute zero at 100 and go from there. I do mean absolute, no "close enough". Once you can smack a small dot at 100, then check your actual drops at distance to see how it line up with a chart. Tweak your input numbers to get them to match you actual drops and then go smack things.
If you are looking for a maximum point blank range for hunting, then a 2 or 3" high zero at 100 will do fine, although your real zero will be set a longer distance.