[eluser]TheFuzzy0ne[/eluser]
Check that there are no spaces after any of the end closing PHP tag on each page. If your server is set to use compression, a simple whitespace after the closing PHP tag will screw it up. I'd bet that your FTP client has added a space to the end of at least one file somewhere.
When writing CodeIgniter apps, it's good practice to simply not bother putting the closing tag in there.
Please check out the CodeIgniter [url="http://ellislab.com/codeigniter/user-guide/general/styleguide.html#php_closing_tag"]PHP Style Guide[/url].
Hope this helps.