It seems to happen if you use any direct rendering with Java2D.

not much you can do atm (not sure Apple even intend to fix it anytime soon), its either get rid of the direct rendering or render your content on a pop out window (i.e. something not embedded in the web page like a JFrame, Frame, etc) or if possible switch to using something like LWJGL applets (which do their own hardware rendering therefore bypass the issue altogether).