I highly doubt this is a bug relating to quartz, but is rather something to do with your setup of applications and log4j. Seems likely to be classpath problems in the apps you are executing via quartz.
I have stored log4j.properties on a separate folder for each app and reread log4j using PropertyConfigurator.configure("d:\\myapp\\log4j.properties") in each time when app runs.
However, when multiple apps runs at the same time, it seems like it reads whatever in the resident memory and apps are stepping on eachother.
Are you suggesting that log4j properties should be stored inside the app?