Domain Mapping using Shared Hosting Directory

Ok, I may simply not have set something correctly, but it seems the Domain Mapping is working correctly with one small problem. All of my pages have now been preceeded by the root directory folder from my hosting company. The domain resolves properly to the home page ( However, every link on the site has the host’s root directory added to it (/~clubfusi/). Is this an installation issue? Is it an htaccess issue?

Frankly, I’m not sure where to start.