We've seen a few customer worried by this log entry in MPControl.log and CCMExec.log when the Configuration Manager site is in native mode. It looks bad, but actually it's a "good" error. We're checking whether the certificate is self-signed, and it's not, so throwing this error. Native mode won't work with a self-signed certificate, so this error is a sign that things are good!
We've answered this question a couple of times on the forums, but still see questions on it - so hopefully posting a blog with the actual error in the title will help people find it more easily.