If you upgrade to vB 4.2, you have to upgrade VaultWiki after it.
For the Configuration Error, you should revisit your server configuration (.htaccess, probably) and make sure wiki_index.php is not passed into another script like vbseo.php. Sorry I can't be more specific without knowing the contents of your configuration.
As for the ACP message, where in the ACP are you seeing this? What did you click, or what form is it under?