The Flash and Java Applets resources are binary files which cannot be processed by any re-writing proxy, including Muse Proxy.
Flash and Java Applets may load in pages re-written by Muse Proxy as long as there are no absolute pathnames in URLs inside them or if there is an object parameter of the Flash or Java Applet, accepting its base URL. However, if the Flash or Java Applet contains links inside them, they will not be re-written.
In other words the Flash and Java Applets may display correctly in Muse Proxy re-written pages, but when an end-user clicks a link hidden inside the Flash or Java Applets it is possible it will go straight to the provider and may appear unauthorized.