Running CodeIgniter from Subfolder on Godaddy

[eluser]yorgo[/eluser]
I found the problem... but not sure as to the solution. I may start a new topic, if one doesn't already exist, but I'll try and give a brief explanation of what's going on.

The problem is with the routing.

I have a few controllers in the application/controllers directory: Index, About, Contact...
They each have an index() and an ajax() function. My default_controller route was set to 'Index' and I added another route for the ajax method like so: $route['rest/(:any)'] = "$1/ajax";

I did also add a contextPath config item for serving the app from a sub-directory. If the path was set I added a couple other routes:
$route[$contextPath] = 'Index';
$route["$contextPath/rest/(:any)"] = "$1/ajax";
$route["$contextPath/(:any)"] = "$1";

This works beautifully locally. Not so nice on GoDaddy.

With the app being served from a sub-directory on GoDaddy, the Index controller cannot be found without adding it to the url. So, www.mydom.com/ci gives a 404 and so does www.mydom.ci/index, while www.mydom.ci/Index loads the Index controller just fine. Also, www.mydom.com/ci/About was found, but www.mydom.com/ci/about gave a 404. Same thing for the contact page, it had to be Contact to find the controller not contact.

WTF GoDaddy?!?!