I got this error in BizTalk:

No Client Certificate matching the provided client certificate hash was found. Verify if the certificate is present in the personal store of the corresponding BizTalk host instance user account.

PLaying with the certificate store, thumbprints did not do anything. So I tried it on another dev machine and the event log showed a different error!

The adapter “FTP” raised an error message. Details “Unable to connect to FTP server “”xxx.xxx.xxx.xxx” as user “username”. Inner Exception details: “The server name in the server certificate does not match with the name of the physical server. Make sure you provide the right server name.

Changing the server in the FTP adapter to the DNS name in the certificate did the trick! Without thumbprint the certificate is correct resolved. So when you encounter certificate error also you can check this.