We had an issue a while back when we installed a JCA connector in WebSphere that came packaged with it's own log4j lib. Since connectors gets loaded into the container classloader hierarchy, the log4j lib in the connector effectively overrode the log4j in our application. It also prevented our own log4j properties from being loaded, since log4j was already bootstrapped.
It would be that you, also, have some other library or resource loaded in your WAS stack that comes with log4j. The way we got around it was doing explicit log4j initialization (reading the log4j properties) programatically in our application.