So to explain some history for you, if your multisite was activated on 3.0 through 3.4, the URLs for subsites would be wp-content/blogs.dir/#/files and the settings would reflect that exactly.
If your multisite was activated AFTER (so 3.5 and up), you get /public_html/wp-content/uploads/sites/2/ but the settings say /public_html/wp-content/uploads/
If you upgraded a multisite from 3.4 to 3.5, however, your urls were not magically changed.
Both installs were fresh. One from 3.7 one from 3.8. No upgrading done. :)
You need to check the httpd.conf file and make sure that "AllowOverride" is set to "All" or "Options All"
Cool, where do I find this file though?
From the godaddy forums:
You cannot edit the httpd.conf file on our web hosting plans. However, most changes can be done using a .htaccess file in the directory you want to the changes to take effect in.
Thanks So Much,
Ken