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I always found this rather annoying fact about applets, that they disappear if you scroll the browser window, to reappear when the scrolling is over. What’s the reason behind this behavior ?
Because Java Applets use the normal/slow 2D capabilities of your graphic card. The fact that the stack is big/complex, OS -> Browser -> Java VM -> Your application does not help either.
Flash applications use 3D acceleration behind the scenes by default, so they do not suffer from this problem since they plug-in into your 3D card directly (bypassing the browser canvas).
You can try running Java2D/applets using 3D acceleration as well, but then you lose the compatibility that Java platform offers (OS agnostic).
http://java.sun.com/j2se/1.5.0/docs/guide/2d/new_features.html