In discussions with ###@###.###, it is clear that the initial JavaScript -> Java call against an applet is being allowed to go through too early. The implicit semantics, which are long-standing, are that the first JS -> Java call is only allowed to be executed once the applet has completed its init() method, unless the applet first makes a Java -> JS call. The fact that fireAppletLoaded() in the Plugin2Manager releases the LiveConnect message queue on the browser side before init() is called is introducing regressions in test cases. This needs to be corrected urgently. It is very likely related to the recent email thread around calls to isActive() causing errors in the IE JavaScript engine.
Please contact ###@###.### for test cases that do JS -> Java calls and which do not behave correctly without a workaround (calling Applet.isActive()) to prevent the JS -> Java call from going through too early.