Your center shot should be the same as it was with a fixed rest. I'm not familiar with your bow, but some require more arrow guidence than others. The fix for some brands is to have the dropaway come up sooner and drop down later. (take some slack out of the cord a little at a time)

Also, are you 100% sure your not getting fletching contact?
Have you tried checking it with lipstick on your fletchings yet? (just put it where you think it would hit the arm if it was hitting, if it's hitting-it'll show up)