From the logback configuration guide (http://logback.qos.ch/manual/configuration.html)
"The property is not declared in the configuration file, thus logback will look for it in the System properties. Java system properties can be set on the command line. "

I believe the precedence should be reversed. Typically, system properties are used to override default values of properties that are specified in XML files or property files (typically checked into source control). Please consider this enhancement. For backwards compatibility you may want to add an option to toggle the precedence ordering.