This is a common problem with some older homes with cast-iron flanges that are just hammered to flare over a flange ring.
The toilet itself is also part of the problem, especially if the bottom of it has a very low waste neck, and does make contact with your flange. Newer toilets actually lift off the ground by a good inch or more, so there is space that is normally filled with the wax ring.
You may want to raise the toilet by what you said half inch. You're going to want to do this with some sort of ring-like base that will lift it up whole, not just shimmed in a few spots. The thick white plastic they use to make kitchen cutting boards is a good material, since it is easy to contour to the shape of your toilet's base.