If you have a div that can go over part of a java applet (though I have noticed this also with flash so I don't know if it is specific to these two or all plugins) and its z-index is the highest, when the applet redraws, it draws over the div and in effect hides it.
Reassigning to webkit-unassigned, to make sure more people see this.
Reporter, could you please file a reduction for this or a url where this bug shows?
This is actually a dupe of 3957. *** This bug has been marked as a duplicate of 3957 ***