Have you upgraded VaultWiki or vBulletin at all since this started happening? If you were using CSS files during the upgrade, it should have rebuilt them. The only way this would happen for CSS files, and not for inline CSS too, is if your CSS file cache is not up-to-date.
Try visiting vault/install/finalupgrade.php while CSS is enabled, and run through the process. You may have to clear your browser cache as well.
I am still not experiencing any issue on my test site and I'm storing CSS as files...
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