From looking through the archives it seems that many people are also facing this problem while trying to embed Jython into their applications.  I'm trying to embed the interpreter into an application that uses its own classloader, and hence, many classes are not on the System classloader.
However, when trying to execute scripts that reside on the non-system classloader, the interpreter is not able to resolve them.  I have tried initializing using the PySystemState.initialize(props, props, args[], classloader), but that did not seem to work either.
I tried using the PySystemState.setClassloader() method as well, which also did not seem to work.
any suggestions?