I was able to reproduce the SYSTEM-job-config-update issue having the following versions:
Jenkins ver. 1.553
Post-Build Script Plug-in plugin ver.0.10
Metadata plugin ver.1.1.0b

The SYSTEM stopped updating job configuration after updating the Post-Build script plugin to ver.0.16:
Jenkins ver. 1.553
Post-Build Script Plug-in plugin ver.0.16
Metadata plugin ver.1.1.0b

It seems that the issue has been fixed somewhere between version 0.10 and 0.16.
Perhaps this change was a fix: https://github.com/jenkinsci/postbuildscript-plugin/commit/b225c1b845bd8b26b153de9fda03dac5c3259b7e ?

I am going to resolve this ticket now.

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