System Center Configuration Manager Team Blog : Known Issue: Logging Information for Native Mode Certificate Selection
We've filed a design change request (DCR) to improve the logging information for future versions of the product, but in the meantime, if you need to confirm which native mode certificate was selected by Configuration Manager, consider running the script that Gabe Brown posted on his blog: Getting a ConfigMgr Client's Registered Certificate Thumbprint.
System Center Configuration Manager Team Blog : Known Issue: Logging Information for Native Mode Certificate Selection