Like all super-nerds I have a thing for cool applications and for beating them into glorious submission. So of course I had a little issue with all the Java incompatibilities with compiz/beryl. There was a discussion of this on the mailing lists, but inevitably most users (like me) will need a little workaround until the issue can be resolved.
Are you ready?
Seriously, here it is.
Just run that before you open your silly java application and the windows should at least appear, there may still be some issues with responsiveness/refreshes, but at least you can see whats happening.