As of 4.0.6, VaultWiki will refuse to install or upgrade if unsafe Zend Opcache configuration settings are detected that might result in the upgrade process executing cached versions of files that were recently uploaded with new updates. This should help workaround the problem some users were having where executing a mix of cached and new files resulted in database corruption.
Please note that the caching issue may still affect the upgrade to 4.0.6 since the 4.0.5 files can still be cached. There is no way to avoid this without the user being proactive and resetting the cache themselves. Upgrades with a previous version of 4.0.6 will display the new warning and instructions to fix the unsafe values.