The EnvInject Plugin needs to manipulate the config.xml of a Job during a build. "EnvInject plugin add technically this line and the line is removed after the run (it is a hack to achieve some plugin objectives)." (JENKINS-14144) Because of this changes scm-sync-configuration spams the repository.

Maybe it is possible to implement a switch for this plugin, to choose if you want to backup changes of "SYSTEM".