In linux, if you check to add Master system configuration (Linux only) and Agent system configuration (Linux only) as well, then the files from master are added twice to the bundle. Because the files from master are also gathered when using _Agent ... _

https://github.com/jenkinsci/support-core-plugin/blob/e2d79249818d41111ea96979a710ac3404018f78/src/main/java/com/cloudbees/jenkins/support/impl/SystemConfiguration.java#L50-L66