[eluser]TheFuzzy0ne[/eluser]
I think that until we can see some source code, it's one of those things that we can discuss until we are blue in the face, and still not find an answer to. Looking at the CodeIgniter source code, there's no way whatsoever that those spaces could be added, unless it's in the developer's code, or the developer has edited a source file.
I'd suggest a fresh copy of CodeIgniter, and if that doesn't work, then please zip up your application directory and post it.