I had the same problem with the seat stay on my Cannondale SR500. A friend made me a spacer out of the strongest piece of plastic I have ever seen in my life. It works perfectly as it gives a very broad surface for the dropout and rack stay attachment points.

You should give Wayne a call at The Touring Store (assuming you are in the U.S.) I think Tibus has kind of a C shaped bracket for the rack that will allow you to get around the stay. But it might move the rack back a bit more than desired as that is the purpose of the bracket. But if you give Wayne a call he will give you good advice.