I am having this same issue and getting mixed information from GoDaddy support. It's very frustrating.
I have applied the fix to main.php as provided (very helpfully) by GoDaddy in this thread which has helped in that most pages now work - with the exception that the homepage fails to load any content with the correct path (it continues to insert index.php/ before all content paths.
the site is two directories in (isolatedangles.com/clients/naomitroski)
The odd thing is that when clicking on links the first time from the homepage it appends the page url twice (http://isolatedangles.com/clients/naomitroski/clients/naomitroski/new-gallery-page/) but then clicking on the link again it calls the correct link (http://isolatedangles.com/clients/naomitroski/new-gallery-page/) ... Basically all links from the homepage are incorrect but off any other page they work fine..
Any ideas?