Hi,
Your site is loading the css correctly. The fact that it has wwwroot in the urls seems to mean your host is doing some weird url forwarding or url masking. You may want to check with them about that because mojoPortal does not usually work correctly with url forwarding or url masking (GoDaddy often does that for subdomains).
The problem why your design is not rendering correctly is not because of CSS failing to load its because the theme.skin file is not being loaded correctly and this makes it not use the special markup needed by Artisteer which is why the menu and other things are not styled as they should be.
This happens under .NET 3.5 in Medium Trust hosting. See the notes about this at the bottom of the article Understanding the theme.skin file. The best solution for the theme.skin problem is to use .NET 4 hosting and the .NET 4 package of mojoPortal.
But aside from the theme.skin problem, the other problems with the urls is due to some url-rewriting/url forwarding/url masking scheme that your host is doing, it just is not going to work that way. This kind of problem has come up before with GoDaddy hosting, see this related thread for one example.
Hope that helps,
Joe