Fedutil not creating passive endpoint for web app

I have a basic claims aware web app that has a WCF service reference. I built it following the steps in the example online and it works. However, I needed to change the site name and update the federation metadata. When I ran fedutil to update the sts reference it did not create the required passive endpoint.  If I comment out the system.serviceModel section and update the sts reference it works correctly.  Is this a bug?