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The best SCEP troubleshooting information that I've encountered can be found in a single TechNet blog post by Mary Hutson. It is a collection of the top Microsoft Support solutions for the most common issues experienced when using System Center 2012 Endpoint Protection and it is updated quarterly.
It contains information and solutions in the following areas:
- Solutions related to malware not cleaned, detected, or quarantined
- Solutions related to SCEP Client Problems
- Solutions related to Definition deployment issues
- Solutions related to Client Policy editing, policy deployment, or policy adherence
- Solutions related to Client Application compatibility (another application has problems)
You can find the blog post here.