How is it possible that a Vault, which is cloned, differs in configuration from the original?
A Vault configuration is changed since the cloning procedure or the new Vault settings are changed after cloning.
Review the Vault logs to pinpoint configuration changes. The logs identify users who make changes and when changes are made.
Only users with permission can review the logs. If needed, open a ticket with Veeva Product Support.
Vault Help Documentation: Viewing Admin Audit Logs