As reported in 6618973, JSObject.call("eval", args) does not work with the new Java Plug-In on Firefox 3. Test case:

3) JSObject.call("eval") throws netscape.javascript.JSException: JavaScript error while calling "eval"
http://sqeweb.sfbay.sun.com/deployment2/jitu/plug-bug/ojiliveconnect/src/JSObjectCallTest.html

This is a bug in the web browser (see https://bugzilla.mozilla.org/show_bug.cgi?id=400771 ) but is one that we can potentially work around in the Java Plug-In, so it is being filed separately.