I made a website for a client and if you go to their URL it loads it up as www.domain.com/ but when you click a link it then makes it www.domain.com/~usernamewithhost/domain.com/ instead of www.domain.com/link-title/

You can see that hear:

http://tinyurl.com/yjpk6q2
(tinyurl for SEO purposes)

Any idea what's causing it to do that? Because if you go to http://tinyurl.com/ykqdqtg you can see a direct link to the site through the host (sonic.net) server. So I'm guessing it has something to do with the host.. but i've never had another CMS do this on Sonic.net hosting. (wordpress/joomla etc).