On the Mac we have to deliver events to the applet process across the communications pipe. Unfortunately, when I did the first implementation for AWT-based applets I put the event delivery methods into PluginEmbeddedFrame. This needs to change so that com.sun.deploy.uitoolkit.Window has methods for receiving the serialized events, which are in turn implemented by PluginEmbeddedFrame.
There will be a corresponding JavaFx change. ID to be added shortly.