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If you have UAC enabled, are you launching the SCCM console in an elevated process? (Right-click > Run as administrator)
When I run config checker, I get the following. I am using internal CA and I have issue a CodeSigning certificate to the User.
I don't get an option to issue a code signing cert for computer account. Not sure what is causing the issue.
The Root CA and code signing certs are present in trusted publisher store.