Only index page is loading

I have developed a Codeignighter app that works great on my local device (windows 7) but when it is loaded to the server (Linux) it only loads the index page. I have tried changing the uri_protocol but that did not work. I also added ? to the index_page attribute. Is there anything else that I can do? Should I make the changes and wait? If so how long? Is there a preferred set-up for Linux Apache servers?

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