Well I feel real stupid, After changing strings I still had the same problem. Called PRS they said short scale 24.5 could be string gauge. I went from 9s back to 10s. Still same problem. I turned the amp off and started looking over things. Played a little unplugged and the harmonics where fine. It ended up being the setting I had on my multi effects board. Turned off the little bit of flange I had on and problem solved.