Used site builder to create website for domain name that has been on Bravenet account for years. When trying to find website under domain name it doesn't come up, but shows up when using the bravesites.com URL address.
Looks like you have found the answer for yourself.
For the benefit of others you have to configure your domain to point to the site that you want to use it with. There are so many possible variations in how you can set things up that the hosting companies do not try and second guess what you want to do.