Sounds similar to the problem I had. the Skin was wrong and I was adding source to programs instead of file system. settings-appearance-skin-confluence and then you should be able to see the layout like on the webpage. you can then scroll over to system and below that will be the file system tab.
Just a heads up for new xbmc installers on iphone. the current cydia install installs with a different skin. leading to all sorts of fun trying to add sources etc. Change it back to confluence and you'll be able to see file system under settings etc.