When you added hosting for the new site, did you use the same FTP user / CGI runs-as user or did you create a new user?
You could be having one of two problems:
1. If you created a new FTP user, you have to upload files as that user.
2. If you reused your existing user, you have to change to the web root directory of your new site.
3. Actually, that makes me think of an alternative potential problem. What did you specify as the web directory for the new domain?
You can find all the settings for your hosted domain by editing the hosting for that domain from the "Domains>Manage Domains" panel.
Free unique IP and $67 off with promo code [color=#CC0000]LMIP67[/color] or use [color=#CC0000]LM97[/color] for $97 off. Click for more promo code discounts