Thread:Project:Support desk/CSS missing from page after removing index.php from url/reply (2)

You say you have a normal php site at the root, but you also have $wgScriptPath set to the root directory. That assumes MediaWiki is installed at the root, but that's not true because you have an alias for /wiki, so it should be /wiki instead.

$wgArticlePath may not be right, also, if you don't have rewrite rules.