There could be a lot of things causing it. Can you post your log configuration file? Do you have a gui project? Are you (or the 3rd party library) attempting to log to gui components?
Are you able to view the log4j configuration files of your 3rd party library?
To address your question of what could be causing this, on the surface, it sounds like they have created a custom logging implementation that is overriding your settings. There are lots of ways to achieve that.
For example, our application at work runs on Tomcat and there's a <logging>
section in the server-config.xml file that allows one to specify a custom logging target for the server.
As another example, I've been bitten dozens of times by rogue commons-logging.properties
files which can change the entire functionality of all logging, application wide, just by modifying a few properties. Further, those files specify a priority flag and if any property file is found on the classpath with a higher priority than the one in your project, it takes precedence!
Overall, there are lots of potential problems here. To be of more assistance, I would need a bit more information.