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So it sounds like in 1.544 the plugin is installed, but not fully functional? Are you sure you configured project-based matrix auth, not global matrix auth? It is working fine for me in a fresh $JENKINS_HOME where I started 1.544, installed Mock Security Realm, configured global security to use Mock Security Realm and Project-Based Matrix Auth, and created a job: the checkbox to enable security for this job was shown as expected.