Remote Desktop Services enrolling for TLS certificate from an Enterprise CA

Hey SokratisZotos 

Sorry I am on vacation still, but wanted to get you an answer on this.

So just based on what you are saying is happening there are basically only two things that can be happening here.

1.  The template that you configured within the GPO is not the certificate templates name.  It is more than likely the certificate templates display name.

2.  The template that you configured within the GPO is configured for autoenrollment on security tab.  

These are the two most common reasons why you are seeing multiple certificates issued.

As far as troubleshooting I would first go into the CA snapin and look at the issue certificates table and locate both of these issued certificates.  were they both issued at the sametime?  Was one issued then several hours later the other one was?  Keep in mind that autoenrollment runs every 8 hours, and if you look at the Certificate Request data it will show you the process name that sent the request to the CA.  based on the process name that generated the CSR to the CA that should give you a pretty good clue as to what is sending the certificate service request to the CA.