I look thru this issue because one of GrinderStone project users report new issue that Java projects are not automatically added to python path during script run: http://code.google.com/p/grinderstone/issues/detail?id=24 I've discovered that problem is in JavaProjectModulesManager which is not return correct PythonPathHelper (see getPythonPathHelper method). Thus I fix this problem locally in my GrinderStone project and I suppose that this fix will be useful for you and should be merged into PyDev codebase. I've attached java source code for extraction all classpath entries from referenced java projects. For more info you can see complete fix: http://code.google.com/p/grinderstone/source/detail?r=139
FYI, GrinderStone http://code.google.com/p/grinderstone is an open source plugin for Eclipse for Grinder performance scripts development and it uses PyDev in a basis.
Complete code to extract PYPATH from referenced Java Projects