[eluser]Majd Taby[/eluser]
ok, unfortunately I'm not on a computer where I can browse my code (i'm off the phone), but what I might have done was hard code the path for the css and javascript assets. Could you please open controllers/codexcontroller.php and search for 'css' and you should see a line that looks something like this:
$this->codextemplates->css(...)
try changing that to use $this->config->item('codex_asset_folder') or something.
if that fixes it, then i'll upload a new release that fixes it shortly.