I had a Hoyt Gamemaster that did that when I would shoot off the shelf; I couldn't get rid of the nock high. When I shot off the elevated rest, it tuned fine. I finally decided that the way it was tillered, it couldn't be tuned to shoot off the shelf. Since I really didn't want to shoot off an elevated rest, I finally sold the bow.
If you want to, you could stick on a cheap flipper rest and see what happens, or just build up the shelf 1/4" or so. At least then you would either know if you had the same problem I did or if it was something else.