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I've run some tests and can't replicate your issue. Could you try installing the snapshot version from https://buildhive.cloudbees.com/job/jenkinsci/job/cvs-plugin/88/org.jenkins-ci.plugins$cvs/artifact/org.jenkins-ci.plugins/cvs/2.9-SNAPSHOT/cvs-2.9-SNAPSHOT.hpi and check what the logs show?
To answer your above comment: The plugin polls the full repository then checks each changed file to see if its path matches the exclude region. I've add in a log message to show which pattern any skipped files have matched to.