Need more info on codeigniter's $config['uri_protocol']

[eluser]intoitdaily[/eluser]
I've been working on a framework of my own and I had never experienced any problems with its clean-url system, but I was migrating some client's codeigniter sites that I developed over to a GoDaddy shared hosting plan, and experienced the whole index.php>>>>>?<<<< "question-mark MUST be at the end" thing and got that fixed no problem. However, I'm experiencing this same exact problem with my own framework when I tested it on the same GoDaddy shared hosting. I was wondering... where and how does codeigniter process the uri protocol? If anyone knows anything more about where this function resides, or how it works, or where I can go to learn more about it... please post it here. Thanks.