@Fergal Cassidy
Thank you for the detailed post!
Based off your issue, this sounds like it could be more of an IIS type issue since everything is working as expected from the Azure Key Vault side of things. When it comes to securing your web server I did find one document - Tutorial: Secure a web server on a Windows virtual machine in Azure with TLS/SSL certificates stored in Key Vault, that might help you with this issue. However, I'd also recommend waiting for our IIS team to take a look into this issue to see if they can provide any insights on this.
Feel free to share any screenshots, so our community can better troubleshoot this issue.
Thank you for your time and patience throughout this issue.