I’m having the same problem, but am not understanding exactly what you did to resolve the problem.
I’ve got WP installed and working in a subfolder on the root directory. I have the domain setup to automatically load WP if anyone goes to my domain. It works fine until I click on another link (on the main blog page) to bring me to another page on the blog. When I do that, the URL changes from my actual domain address to the weird NS’s address.
How do I fix this?