If it is still showing 3.0.6, that means that you are still using the 3.0.6 version of the vault/wiki.php file which controls vBulletin version detection.
By looking at the CSS it is trying to use, it looks like VaultWiki's 3.0.6 file is reporting your version as < vB 4.0.0. We released 3.0.7 because of this exact issue.
In our Members Area, the default download options give you only files that are different from your last download, so you may need to select other options. Where it asks "Only download files changed since", select "3.0.6 Build 001".