So there I was, poking around in some java / j2ee code, trying to learn how it all works. I did some testing on a Linux server and realized, something is broken. It seemed something was corrupting ALL the Jar files in WEB-INF/lib/. A co-worker guessed that the token filtering Ant was doing might be the culprit. He was right. It seems Ant has issues with detecting whether files are binary or not, given that it uses a Reader class which runs the files through a character decoder.