5) I think the biggest problem is using FindClass() under Webstart.
Developers are expecting to be able to take a standalone Java
application, wrap it using Webstart and deploy it. No one expects that
Webstart uses a custom class-loader which breaks the way native code
works so a lot of work needs to go into documenting this better so
developers know how to code in a manner that is portable across Webstart
and stand-alone applications.

I think it would be useful to add a section to
http://java.sun.com/j2se/1.5.0/docs/guide/javaws/developersguide/contents.html
which explicitly discusses Webstart's custom classloader and its impacts
on JNI code (i.e. "how to write JNI code which is Webstart-safe").
Jacob(###@###.###) is the writer for Java Web Start and will be resolving this bug.
I fixed this bug in coordination with Andy Herrick. I added one more query to the FAQ, updated the faq.html page and did putback.