Since moving to Gutsy, I've been seeing this issue where java apps loaded from Firefox are coming up as blank screens, or with weird effects.
I am running the compiz-fusion desktop effects, but I had this issue even if they were disabled. I think it probably has to do with the XGL I'm running (to solve another issue)
I checked to make sure that I was running the sun java implementation, which I am. so I was getting stumped, but I found a post (somewhere - I lost the link sorry) which suggested removing the gcjwebplugin. This plugin is "a little web browser plugin to execute Java applets". I suspect that it was calling the GCJ (opensource java) instead of the Sun Java i had installed. Simply removing that via synaptic did the trick for me.