Customer's application uses Microsoft's Remote Scripting (MSRS).  MSRS uses JavaScript on the client side to communicate with an applet (RSProxy.class, Microsoft's applet).  The applet is then used to invoke methods on a server-side ASP and send the server's response back to the client.  The issue is that the Sun JVM prevents their application from receiving Windows messages off the message queue.  They are trying to run a script that will bring up a new native window, but that window never appears.

The application works with the Microsoft JVM.  It also worked up to 1.3.1_02 and 1.4.0, but is broken from 1.3.1_03 and 1.4.0_01 onwards.  I believe this is related to the fix for bug 4506751.  This fix involved adding the WaitWithMessageLoop function to CDispatch.cpp, which calls PeekMessage with a NULL window handle.  In bug 4802147, the NULL handle was changed to the handle for the control window.  However, the problem still exists in 1.3.1_08.

The customer's code also contains a function which calls PeekMessage with a NULL window handle.  It appears that since the JVM retrieves the Windows messages off the queue, the customer's app just sits in an infinite loop waiting for a message which it never receives.  The customer's app is waiting for messages in their application's COM control which is inside a browser frame.  They don't believe this should be the same as the JVM's control window since the JVM is not used within this frame, but somehow the JVM seems to be interfering anyway.