System Center Endpoint Protection 2012 R2 policy issue

Recently I came across this issue about SCEP update definitions not being applied on (in my case) Citrix VDI computers.

Errors in the C:\Windows\CCM\Logs\EndpointProtectionAgent.log
Failed to apply the policy C:\WINDOWS\CCM\EPAMPolicy.xml with error (0x80004005).
Failed to apply policy with error 0x80004005, retry number : 1 after 60 second.

But mainly visible in the Management Console.

Luckily there are some community colleagues who dealt with this issue before, I did not solve my issue, maybe because we use streamed vDisk, or because this issue already existed for a long time. Any way many people benefit from the solution.

See Henk's blog for a solution.

Edit: Another solution could be to remove the gpt.ini (C:\Windows\System32\grouppolicy) because it became corrupt.