I spent most of yesterday trying to drill into this issue, and when I finally got into debugging the sun.misc.* URLClassLoader related stuff, the problem disappeared when I hooked up the current jrl source code as the bootclasspath. I can't tell exactly what release of the jdk this code corresponds to though. This code is wrapping our vfsfile urls in jar urls and creating tmp jar files for this, so its duplicating the work we are trying to do. I'm inclined to ignore this issue until the new non-URLClassLoader changes are in as we seem to be fighting with implementation detail assumptions made at the URLClassLoader layer.
The vfs url handler needs to be changed anyway for these issues:
Once that is done I'll revisit the URLClassLoader interaction to see if its more obvious why the view is getting out of sync.