I've been using a lot of Flash in my PowerPoint stuff lately. I find that if you select your background, then use flat 100% transparency, then convert to Flash. This works pretty well, especially if the background is roughly similar to the one on which it will be going. (Transparent black on a white background sometimes looks like a wall that needs to be cleaned.)

Of course this only works when you make your own Flash...LOL

I have also tried using the same background for my animation that I am using for the PowerPoint slide, making it appear virtually seamless.

My third option is to simply put a decorative frame around the animation. Sometimes, you need a particular background for the animtion to work with the theme, but you might not want this to cover the whole screen!
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Will