Mouse keeps flickering?

Whenever I do some kind of animation in Java 3D (I’m worried it’s going to happen with 2D animation, too) my mouse always flickers and then comes back very rapidly. Does this have anything to do with the application updating itself, and it’s doing it over the mouse? Whenever this happens the application is (usually) using a timer for animation. Is this a good way to animate things and could this be what’s causing my mouse problem? Thanks.