I spent nearly an hour for banging over the issue that on Websphere application server the logs were not getting written.
Finally, I found out someone had created a zip file of the log4j.xml and kept it as a back up file. This was being picked up by the server.
This made me search for some configuration in log4j, which would output the logs from log4j itself.
What you need to do is add a JVM property like this:
-Dlog4j.debug
When the application starts, now we can see which file is actually being loaded for logger configuration.