I have a 2008 Server R2 setup on which I am configuring Auto Enrollment. I am using an External CA for issuing certs. While issuing a computer certificate from a template, Root CA cert is getting published to Intermediate Certificate Store.
Issuing CA is published to Intermediate Certificate Store as expected.
While this can be easily cleaned up the situation would repeat itself when Autoenrollment is triggered next. I am using DCOM interface to connect.
Any pointers would be useful in resolving above issue.