The CLASSPATH is an environment variable that you set yourself somewhere, in a configuration file or startup or login script. The system does not automatically set it for you. The Linux kernel does not have anything to do with your CLASSPATH.
You must have slightly different configuration / startup / login scripts on the two systems somewhere.
By the way, it's not a good idea to write Java programs that rely on the fact that things in the CLASSPATH are in a certain order - it makes your program very susceptible to small system configuration changes. [ November 08, 2006: Message edited by: Jesper Young ]