Thanks for the quick response. The issue I had, and you verified what I had hoped, was that the eval board that we are testing with was designed for +5 out. So on the board the two grounds are connected. By changing the circuit up and switching our references on the output side, I thought we would have issues integrating it with the other supplies. What I did was the lift all the input caps and connect them to the Vout+(the new ground) and connect all gnds to a common point. This will work fine for our preliminary testing.
Again, thanks for the timely response.