The bug is easier reproducible with kernel vm. Install kernel jre (jre...-k.exe). As soon as installer is done, launch MoleculeViewer applet in IE7. When you see "Additional Components" download dialog, while applet has not loaded yet, click "Reload" button in the browser multiple times. Make sure Java Console is set to "Open" in your deployment.properties file - this way you'll see exception printed.
java.awt.IllegalComponentStateException: Native resources unavailable
   at sun.awt.windows.WPanelPeer.pRestack(Native Method)
   at sun.awt.windows.WPanelPeer.restack(Unknown Source)
   at sun.awt.windows.WWindowPeer.restack(Unknown Source)
   at java.awt.Container.addNotify(Unknown Source)
   at java.awt.Window.addNotify(Unknown Source)
   at java.awt.Frame.addNotify(Unknown Source)
   at sun.awt.EmbeddedFrame.addNotify(Unknown Source)
   at sun.awt.windows.WEmbeddedFrame.addNotify(Unknown Source)
   at sun.plugin2.main.client.PluginEmbeddedFrame.addNotify(Unknown Source)
   at sun.awt.windows.WEmbeddedFrame.<init>(Unknown Source)
   at sun.plugin2.main.client.PluginEmbeddedFrame.<init>(Unknown Source)
   at sun.plugin2.main.client.PluginMain$StartAppletRunner.run(Unknown Source)
   at java.awt.event.InvocationEvent.dispatch(Unknown Source)
   at java.awt.EventQueue.dispatchEvent(Unknown Source)
   at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
   at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
   at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
   at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
   at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
   at java.awt.EventDispatchThread.run(Unknown Source)
PluginMain: could not create embedded frame

After this exception occurs I am unable to load any applets, the browser has to be restarted. Noticed the problem in b27.